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Zhao, Qiong, Fengxing Xie, Fengfeng Zhang, Ke Zhou, Haibo Sun, Yujie Zhao, and Qian Yang. "Analysis of bacterial community functional diversity in late-stage shrimp (Litopenaeus vannamei) ponds using Biolog EcoPlates and PICRUSt2." Aquaculture 546 (January 2022): 737288. http://dx.doi.org/10.1016/j.aquaculture.2021.737288.
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Baltazar-Díaz, Tonatiuh Abimael, Luz Alicia González-Hernández, Juan Manuel Aldana-Ledesma, Marcela Peña-Rodríguez, Alejandra Natali Vega-Magaña, Adelaida Sara Minia Zepeda-Morales, Rocío Ivette López-Roa, et al. "Escherichia/Shigella, SCFAs, and Metabolic Pathways—The Triad That Orchestrates Intestinal Dysbiosis in Patients with Decompensated Alcoholic Cirrhosis from Western Mexico." Microorganisms 10, no. 6 (June 16, 2022): 1231. http://dx.doi.org/10.3390/microorganisms10061231.
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Gut microbiota undergoes profound alterations in alcohol cirrhosis. Microbiota-derived products, e.g., short chain fatty acids (SCFA), regulate the homeostasis of the gut-liver axis. The objective was to evaluate the composition and functions of the intestinal microbiota in patients with alcohol-decompensated cirrhosis. Fecal samples of 18 patients and 18 healthy controls (HC) were obtained. Microbial composition was characterized by 16S rRNA amplicon sequencing, SCFA quantification was performed by gas chromatography (GC), and metagenomic predictive profiles were analyzed by PICRUSt2. Gut microbiota in the cirrhosis group revealed a significant increase in the pathogenic/pathobionts genera Escherichia/Shigella and Prevotella, a decrease in beneficial bacteria, such as Blautia, Faecalibacterium, and a decreased α-diversity (p < 0.001) compared to HC. Fecal SCFA concentrations were significantly reduced in the cirrhosis group (p < 0.001). PICRUSt2 analysis indicated a decrease in acetyl-CoA fermentation to butyrate, as well as an increase in pathways related to antibiotics resistance, and aromatic amino acid biosynthesis. These metabolic pathways have been poorly described in the progression of alcohol-related decompensated cirrhosis. The gut microbiota of these patients possesses a pathogenic/inflammatory environment; therefore, future strategies to balance intestinal dysbiosis should be implemented. These findings are described for the first time in the population of western Mexico.
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Ponomareva, E. S., E. A. Yildirim, V. A. Filippova, L. A. Ilina, A. V. Dubrowin, G. Y. Laptev, K. A. Kalitkina, T. P. Dunyashev, and D. G. Tiurina. "Comparison of the composition and metabolic potential of the reindeer’s rumen microbiome in the Yamal-Nenets and Nenets autonomous district of the Russian Arctic." Acta Biomedica Scientifica 7, no. 3 (July 5, 2022): 30–37. http://dx.doi.org/10.29413/abs.2022-7.3.4.
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The adaptive ability of reindeer to the harsh conditions of the Russian Arctic is not determined solely by the genome of the macroorganism and, of course, includes an extensive genetic and metabolic repertoire of the microbiome.The aim. To compare the taxonomic and predicted metabolic profiles of the rumen microbiome of adult reindeer living in the natural pastures of the Yamalo-Nenets and Nenets Autonomous districts of the Russian Federation.Materials and methods. Expeditions to the Yamal-Nenets and Nenets Autonomous districts of the Russian Arctic in 2017 were carried out to take samples of the rumen. The contents of the rumen were taken from clinically healthy reindeer individuals (at least 3 times repetition). To analyze the animal scar microbiota and determine metabolic profiles, 16S rRNA NGS sequencing was performed on a MiSeq device (Illumina, USA). Bioinformatic data analysis was performed using QIIME2 software ver. 2020.8. The noise sequences were filtered by DADA2. Silva 138 reference database was used for taxonomy analysis. Reconstruction and prediction of the functional content of the metagenome was carried out using the software complex PICRUSt2 (v. 2.3.0).Results. During NGS sequencing, a total of 223 768 sequences of the 16S rRNA gene of the reindeer scarring microbiome were studied. Significant (p ≤ 0.05) differences between the groups in 10 bacterial phyla and superphyla were revealed: Actinobacteriota, Spirochaetes, Chloroflexi, Verrucomicrobia, Bdellovibrionota, Synergistetes, Fusobacteriota, Myxococcota, Cyanobacteria, Campilobacterota. The results of the reconstruction and prediction of the functional content of the metagenome using the PICRUSt2 bioinformatic analysis made it possible to identify 328 potential metabolic pathways. Differences between the groups were revealed in 16 predicted metabolic pathways, among which the pathways of chlorophyllide and amino acid biosynthesis dominated.
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Jeong, Su-Ji, Myeong-Seon Ryu, Hee-Jong Yang, Xuan-Hao Wu, Do-Youn Jeong, and Sun-Min Park. "Bacterial Distribution, Biogenic Amine Contents, and Functionalities of Traditionally Made Doenjang, a Long-Term Fermented Soybean Food, from Different Areas of Korea." Microorganisms 9, no. 7 (June 22, 2021): 1348. http://dx.doi.org/10.3390/microorganisms9071348.
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Since doenjang quality depends on the bacterial composition, which ambient bacteria in the environment and production conditions influence, a complete understanding of the bacteria community in traditionally madetraditionally made doenjang (TMD) from different regions is needed. We aimed to investigate the bacteria composition and quality of TMD in the following areas: Chonbuk (CB), Chonnam (CN), Kyungsang (KS), Kangwon (KW), Chungchung (CC) provinces, and Jeju island (JJ) of Korea. Twenty-nine TMD samples from different regions were used to assess biogenic amine contents, bacteria composition using next-generation methods, and metabolic functions of the bacteria using Picrust2. Bacillus spp. were isolated, and their antioxidant and fibrinolytic activities were determined. Most TMD contained high amounts of beneficial bacteria (Bacillus, Lactobacillus, Pediococcus and Weissella). However, some KS samples contained harmful bacteria (Cronobacter, Proteus and Acinetobacter) and less beneficial B. velezensis bacteria. There was no similarity among the regional groups, and each TMD showed a different bacteria composition. Shannon index, α-diversity index, was lower in TMD from JJ and CB than the other areas, but there was no β-diversity among TMD from the six area groups. Picrust2 analysis revealed that the functional potential for arachidonic acid metabolism was lowest in JJ and CN, that for supporting insulin action was highest in KS and JJ, and that for carbohydrate digestion and absorption was lowest in CB and JJ among all groups (p < 0.05) according to the Kyoto Encyclopedia of Genes and Genomes Orthology. Histamine contents were lower in CN and CC, and tyramine contents did not differ significantly. B. velezensis, B. subtilis, B. licheniformis, B. siamensis, and B. amyloliquefaciens were isolated from TMD. None of the isolated Bacillus spp. contained the B. cereus gene. B. subtilis from CN had the highest fibrinolytic activity, and B. velezensis from CB had the highest antioxidant activity. In conclusion, TMD mainly contained various Bacillus spp., and the predominant one was B. velezensis, which had antioxidant and fibrinolytic activity regardless of the regional origin.
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Guo, Manli, Zhidong Zhang, Jiyuan Lu, Di Wang, Yimin Yan, Shen Zhang, Xin Yu, et al. "Differences in Supragingival Microbiome in Patients with and without Full-Crown Prostheses." Dentistry Journal 10, no. 8 (August 15, 2022): 152. http://dx.doi.org/10.3390/dj10080152.
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Objectives: To characterize the microflora profile of supragingival biofilm in patients with and without full-crown prostheses. Methods: Plaque samples of full-crown prostheses and teeth in patients with porcelain-fused-to-metal crowns, all-ceramic crowns, and no prostheses were collected (three patients per group), using 16S rRNA high-throughput sequencing technology to conduct DNA sequencing on the samples and using Qiime, R, and PICRUSt2 software to perform bioinformatics analyses and functional analyses on sequencing data. Results: In total, 110,209 valid sequences were obtained in the experiment, corresponding to 11 phyla and 120 genera. The predominant species shared by the three groups were phyla Actinobacteria, Bacteroidetes, Firmicutes, Fusobacteria, and Proteobacteria and genera Rothia, Porphyromonas, Prevotella, Streptococcus, Veillonella, Leptotrichia, Neisseria, Citrobacter, and Pseudomonas. The species-difference analysis showed that genus Hameophilus significantly increased after the patient wore the dental prosthesis. Compared with the no-prosthesis samples, the functional analysis showed that cell motility increased in the samples from full-crown prostheses, while replication and repair, and translation decreased. Conclusions: This study reveals the changes in the oral microbial community of patients with full-crown prostheses, which could provide insights regarding the safety of materials for long-term use in the oral cavity.
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Bierwirth, S., A. Sorbie, O. Coleman, E. Reuß, P. Weber, N. Köhler, T. Kacprowski, et al. "P057 Mucosal microbiota adapts to ATF6-induced alterations in host lipid metabolism with prognostic value in colorectal cancer." Journal of Crohn's and Colitis 16, Supplement_1 (January 1, 2022): i167. http://dx.doi.org/10.1093/ecco-jcc/jjab232.186.
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Abstract Background Colorectal cancer (CRC) is a leading cause of cancer deaths worldwide. The endoplasmic reticulum unfolded protein response (UPRER) signal transducer activating transcription factor 6 (ATF6) is a clinically relevant pre-cancerous marker in CRC and colitis-associated CRC. We established the interrelated role of the microbiota and ATF6 signalling as a novel tumor-promoting mechanism in our transgenic mouse model of spontaneous microbiota-dependent ATF6-driven CRC (nATF6IEC). Methods To elucidate the transcriptional program initiated by acute and chronic ATF6 signalling, mRNA sequencing analyses of murine colonic intestinal epithelial cells were performed 4 days or 5 weeks after induction of ATF6, respectively. Germfree (GF) mice served to dissect microbiota contribution to the transcriptional response. CRC patient datasets (TCGA) were used to estimate ATF6 activity and validate ATF6-driven signatures. To investigate the impact of ATF6 signalling on metabolites, untargeted metabolomics of faeces and targeted lipidomics of tissue were performed. Mucosal microbiota was spatially characterised by 16S rRNA profiling at mm resolution along the colonic longitudinal axis. Based on 16S rRNA data, Phylogenetic Investigation of Communities Reconstruction of Unobserved States (PICRUSt2) was used to infer microbiota lipid-specific functional content. Results We identified an ATF6-UPR core of 368 differentially expressed genes fully activated by acute ATF6 signalling. Functional analysis using KEGG pathways showed that chronic ATF6 signalling predominantly alters UPR-related and metabolic pathways, with 22% of metabolic pathway genes classified as lipid metabolism. GF mice confirmed that the microbiota enhances ATF6-induced metabolic changes. Kaplan-Meier analyses significantly associate our microbiota-dependent ATF6-driven and lipid-specific ATF6-driven gene signatures with decreased disease-free survival in CRC patients since primary therapy. Moreover, ATF6 activity correlates with the presence of CRC-associated bacteria in TCGA samples. Tumor-susceptible mice show alterations in lipid metabolites, particularly long-chain fatty acids (FA) and elongation of saturated FA. PICRUSt2 revealed bacterial lipid detoxification mechanisms, with an increased total abundance of oleate hydratase-positive species. Conclusion Chronic ATF6-signalling alters host lipid metabolism and the lipid milieu in tumor-developing nATF6IEC mice. ATF6-driven microbiota changes are concomitant with bacterial lipid detoxification mechanisms in the tumor niche. We postulate that chronic ATF6 signalling represents a clinically relevant pathologic response that alters the intestinal lipid milieu and thus selects for a tumor-promoting microbiota.
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Warinner, James, Mohamed ElSaadani, Kian Rosenau, Jong Hyun Kim, Syed Adeel Hassan, Sarayu Bhogoju, Lesley Wempe, et al. "AUPHOS, A NOVEL DRUG THAT IMPROVES COLITIS BY MICROBIOME INDUCED METABOLIC CHANGES." Inflammatory Bowel Diseases 29, Supplement_1 (January 26, 2023): S49. http://dx.doi.org/10.1093/ibd/izac247.094.
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Abstract BACKGROUND Dysbiotic intestinal microbiomes dominated by facultative anaerobes are strongly associated with inflammatory bowel disease (IBD). More recently, data from Baumler and colleagues support a model where mitochondrial dysfunction causes disease-associated dysbiosis by increasing oxygen (O2) availability to the microbiome. We posit that the restoration of epithelial mitochondrial respiration contributes to the restoration of a healthy microbiome dominated by facultative anaerobes such as Firmicutes [that produce short chain fatty acids (SCFA)]. Here, we tested a novel compound (AuPhos) that increases an O2 consumption in intestinal epithelial cells (IECs) thereby reducing O2 availability to the microbiome and promotes a healthy anaerobic environment (and blooms of firmicutes). METHOD Inbred C57BL/6 mice (n=3) were given oral vehicle (0.5% DMSO/Tween-80) or AuPhos (2.5 or 25mg/Kg;q3d) for two weeks, and colon and stool samples were extracted at day-15 sacrifice. Microbial DNA was isolated from stool samples using PoweFecal kit followed by 16S rRNA metagenomic sequencing. Linear Discriminant Analysis (LDA) and PICRUST2 were performed to reveal differentially abundant bacterial species and functional potentials of bacterial communities, respectively. Similar microbial profiling was performed on AuPhos-fed acute colitis mice (2% DSS-7d; Recovery-16d). Effect of AuPhos on microbial metabolism was determined by 1H NMR for detecting SCFA synthesis by gut microbiota in stool samples (n=3) collected after 3 consecutive doses. AuPhos-induced hypoxia in IECs was assessed by Hypoxyprobe-1 kit. RESULT Metagenomic analysis showed reduction in relative abundance of (O2 consuming) Proteobacteria and facultatively anaerobic Enterobacteriaceae in the gut, in AuPhos-fed mice. Conversely, AuPhos treatment dose- dependently increased the relative abundance of signature anaerobic bacteria e.g. Firmicutes including Clostridia (Faecalibacterium prausnitzii, Roseburia sp.), Bifidobacterium, etc. PICRUST2 and LDA revealed that AuPhos decreased bacterial LPS biosynthetic pathway and increased overall fatty acid biosynthesis pathways. AuPhos increased butyrate and propionate levels by >35% and acetate by 60% (n=3) compared to stools from vehicle-treated mice. In DSS-colitis mice, AuPhos reduced the relative abundance of inflammatory Proteobacteria, which includes facultative anaerobic Enterobacteriaceae family and increased Firmicutes over time (p<0.05). Interestingly, hypoxia staining showed AuPhos-induced O2 utilization in colonic surface IECs, facilitating obligate anaerobe-promoting environment in the gut. CONCLUSION These finding suggest that AuPhos is a “first-in-class” oral therapeutic that has a potential to correct microbial dysbiosis in IBD by reducing epithelial oxygenation and thereby promoting a healthy microbiome dominated by obligate anaerobes.
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Yuan, Huatao, Tangcheng Li, Hongfei Li, Cong Wang, Ling Li, Xin Lin, and Senjie Lin. "Diversity Distribution, Driving Factors and Assembly Mechanisms of Free-Living and Particle-Associated Bacterial Communities at a Subtropical Marginal Sea." Microorganisms 9, no. 12 (November 27, 2021): 2445. http://dx.doi.org/10.3390/microorganisms9122445.
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Free-living (FL) and particle-associated (PA) bacterioplankton communities play critical roles in biogeochemical cycles in the ocean. However, their community composition, assembly process and functions in the continental shelf and slope regions are poorly understood. Based on 16S rRNA gene amplicon sequencing, we investigated bacterial communities’ driving factors, assembly processes and functional potentials at a subtropical marginal sea. The bacterioplankton community showed specific distribution patterns with respect to lifestyle (free living vs. particle associated), habitat (slope vs. shelf) and depth (surface vs. DCM and Bottom). Salinity and water temperature were the key factors modulating turnover in the FL community, whereas nitrite, silicate and phosphate were the key factors for the PA community. Model analyses revealed that stochastic processes outweighed deterministic processes and had stronger influences on PA than FL. Homogeneous selection (Hos) was more responsible for the assembly and turnover of FL, while drift and dispersal limitation contributed more to the assembly of PA. Importantly, the primary contributor to Hos in PA was Gammaproteobacteria:Others, whereas that in FL was Cyanobacteria:Bin6. Finally, the PICRUSt2 analysis indicated that the potential metabolisms of carbohydrates, cofactors, amino acids, terpenoids, polyketides, lipids and antibiotic resistance were markedly enriched in PA than FL.
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Yasuda, Michiko, Khondoker M. G. Dastogeer, Elsie Sarkodee-Addo, Chihiro Tokiwa, Tsuyoshi Isawa, Satoshi Shinozaki, and Shin Okazaki. "Impact of Azospirillum sp. B510 on the Rhizosphere Microbiome of Rice under Field Conditions." Agronomy 12, no. 6 (June 5, 2022): 1367. http://dx.doi.org/10.3390/agronomy12061367.
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There has been increasing attention toward the influence of biofertilizers on the composition of microbial communities associated with crop plants. We investigated the impact of Azospirillum sp. B510, a bacterial strain with nitrogen-fixing ability, on the structure of bacterial and fungal communities within rice plant rhizospheres by amplicon sequencing at two sampling stages (the vegetative and harvest stages of rice). Principal coordinate analysis (PCoA) demonstrated a significant community shift in the bacterial microbiome when the plants were inoculated with B510 at the vegetative stage, which was very similar to the effect of chemical N-fertilizer application. This result suggested that the inoculation with B510 strongly influenced nitrogen uptake by the host plants under low nitrogen conditions. Least discriminant analysis (LDA) showed that the B510 inoculation significantly increased the N2-fixing Clostridium, Aeromonas and Bacillus populations. In contrast, there was no apparent influence of B510 on the fungal community structure. The putative functional properties of bacteria were identified through PICRUSt2, and this hinted that amino acid, sugar and vitamin production might be related to B510 inoculation. Our results indicate that B510 inoculation influenced the bacterial community structure by recruiting other N2-fixing bacteria in the absence of nitrogen fertilizer.
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Yuan, Xiangqun, Xuan Zhang, Xueying Liu, Yanlu Dong, Zizheng Yan, Dongbiao Lv, Ping Wang, and Yiping Li. "Comparison of Gut Bacterial Communities of Grapholita molesta (Lepidoptera: Tortricidae) Reared on Different Host Plants." International Journal of Molecular Sciences 22, no. 13 (June 25, 2021): 6843. http://dx.doi.org/10.3390/ijms22136843.
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Intestinal symbiotic bacteria have played an important role in the digestion, immunity detoxification, mating, and reproduction of insects during long-term coevolution. The oriental fruit moth, Grapholita molesta, is an important fruit tree pest worldwide. However, the composition of the G. molesta microbial community, especially of the gut microbiome, remains unclear. To explore the differences of gut microbiota of G. molesta when reared on different host plants, we determined the gut bacterial structure when G. molesta was transferred from an artificial diet to different host plants (apples, peaches, nectarines, crisp pears, plums, peach shoots) by amplicon sequencing technology. The results showed that Proteobacteria and Firmicutes are dominant in the gut microbiota of G. molesta. Plum-feeding G. molesta had the highest richness and diversity of gut microbiota, while apple-feeding G. molesta had the lowest. PCoA and PERMANOVA analysis revealed that there were significant differences in the gut microbiota structure of G. molesta on different diets. PICRUSt2 analysis indicated that most of the functional prediction pathways were concentrated in metabolic and cellular processes. Our results confirmed that gut bacterial communities of G. molesta can be influenced by host diets and may play an important role in host adaptation.
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Zhao, Qingyu, Dianzhi Hou, Yongxia Fu, Yong Xue, Xiao Guan, and Qun Shen. "Adzuki Bean Alleviates Obesity and Insulin Resistance Induced by a High-Fat Diet and Modulates Gut Microbiota in Mice." Nutrients 13, no. 9 (September 17, 2021): 3240. http://dx.doi.org/10.3390/nu13093240.
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Adzuki bean consumption has many health benefits, but its effects on obesity and regulating gut microbiota imbalances induced by a high-fat diet (HFD) have not been thoroughly studied. Mice were fed a low-fat diet, a HFD, and a HFD supplemented with 15% adzuki bean (HFD-AB) for 12 weeks. Adzuki bean supplementation significantly reduced obesity, lipid accumulation, and serum lipid and lipopolysaccharide (LPS) levels induced by HFD. It also mitigated liver function damage and hepatic steatosis. In particular, adzuki bean supplementation improved glucose homeostasis by increasing insulin sensitivity. In addition, it significantly reversed HFD-induced gut microbiota imbalances. Adzuki bean significantly reduced the ratio of Firmicutes/Bacteroidetes (F/B); enriched the occurrence of Bifidobacterium, Prevotellaceae, Ruminococcus_1, norank_f_Muribaculaceae, Alloprevotella, Muribaculum, Turicibacter, Lachnospiraceae_NK4A136_group, and Lachnoclostridium; and returned HFD-dependent taxa (Desulfovibrionaceae, Bilophila, Ruminiclostridium_9, Blautia, and Ruminiclostridium) back to normal status. PICRUSt2 analysis showed that the changes in gut microbiota induced by adzuki bean supplementation may be associated with the metabolism of carbohydrates, lipids, sulfur, and cysteine and methionine; and LPS biosynthesis; and valine, leucine, and isoleucine degradation.
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Batool, Maria, Ciara Keating, Sundus Javed, Arshan Nasir, Muhammad Muddassar, and Umer Zeeshan Ijaz. "A Cross-Sectional Study of Potential Antimicrobial Resistance and Ecology in Gastrointestinal and Oral Microbial Communities of Young Normoweight Pakistani Individuals." Microorganisms 11, no. 2 (January 20, 2023): 279. http://dx.doi.org/10.3390/microorganisms11020279.
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Antimicrobial resistance (AMR) is a major global public health concern mainly affecting low- and middle-income countries (LMICs) due to lack of awareness, inadequate healthcare and sanitation infrastructure, and other environmental factors. In this study, we aimed to link microbial assembly and covariates (body mass index, smoking, and use of antibiotics) to gut microbiome structure and correlate the predictive antimicrobial gene prevalence (piARG) using PICRUSt2. We examined the gastrointestinal and oral microbial profiles of healthy adults in Pakistan through 16S rRNA gene sequencing with a focus on different ethnicities, antibiotic usage, drinking water type, smoking, and other demographic measures. We then utilised a suite of innovative statistical tools, driven by numerical ecology and machine learning, to address the above aims. We observed that drinking tap water was the main contributor to increased potential AMR signatures in the Pakistani cohort compared to other factors considered. Microbial niche breadth analysis highlighted an aberrant gut microbial signature of smokers with increased age. Moreover, covariates such as smoking and age impact the human microbial community structure in this Pakistani cohort.
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Palmieri, Orazio, Stefano Castellana, Giuseppe Biscaglia, Anna Panza, Anna Latiano, Rosanna Fontana, Maria Guerra, et al. "Microbiome Analysis of Mucosal Ileoanal Pouch in Ulcerative Colitis Patients Revealed Impairment of the Pouches Immunometabolites." Cells 10, no. 11 (November 19, 2021): 3243. http://dx.doi.org/10.3390/cells10113243.
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The pathogenesis of ulcerative colitis (UC) is unknown, although genetic loci and altered gut microbiota have been implicated. Up to a third of patients with moderate to severe UC require proctocolectomy with ileal pouch ano-anastomosis (IPAA). We aimed to explore the mucosal microbiota of UC patients who underwent IPAA. Methods: For microbiome analysis, mucosal specimens were collected from 34 IPAA individuals. Endoscopic and histological examinations of IPAA were normal in 21 cases, while pouchitis was in 13 patients. 19 specimens from the healthy control (10 from colonic and 9 from ileum) were also analyzed. Data were analyzed using an ensemble of software packages: QIIME2, coda-lasso, clr-lasso, PICRUSt2, and ALDEx2. Results: IPAA specimens had significantly lower bacterial diversity as compared to normal. The microbial composition of the normal pouch was also decreased also when compared to pouchitis. Faecalibacterium prausnitzii, Gemmiger formicilis, Blautia obeum, Ruminococcus torques, Dorea formicigenerans, and an unknown species from Roseburia were the most uncommon in pouch/pouchitis, while an unknown species from Enterobacteriaceae was over-represented. Propionibacterium acnes and Enterobacteriaceae were the species most abundant in the pouchitis and in the normal pouch, respectively. Predicted metabolic pathways among the IPAA bacterial communities revealed an important role of immunometabolites such as SCFA, butyrate, and amino acids. Conclusions: Our findings showed specific bacterial signature hallmarks of dysbiosis and could represent bacterial biomarkers in IPAA patients useful to develop novel treatments in the future by modulating the gut microbiota through the administration of probiotic immunometabolites-producing bacterial strains and the addition of specific prebiotics and the faecal microbiota transplantation.
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Dania, Margaret I., Bahram Faraji, and James Wachira. "Micronutrient Biosynthesis Potential of Spontaneous Grain Fermentation Microbiomes." International Journal of Environmental Research and Public Health 19, no. 24 (December 10, 2022): 16621. http://dx.doi.org/10.3390/ijerph192416621.
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Fermented foods play an important role in the human diet and particularly so in under-resourced environments where cold preservation is not attainable due to irregular supply of electricity. Fermented foods are reported to support gut health by contributing probiotics. The purpose of this study was to investigate the microbial diversity and metabolic potential of spontaneous millet fermentation. The literature in the field was reviewed and analyses were conducted on publicly available Sequence Read Archive (SRA) datasets. Quality analysis was performed with FastQC, and operational taxonomic units (OTUs) were generated using Quantitative Insights Into Microbial Ecology (QIIME2) and Divisive Amplicon Denoising Algorithm (DADA2) pipelines with Greengenes as the reference database. Metagenomics and pathways analysis were performed with Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt2). Statistical analysis and visualization were accomplished with Statistical Analysis of Metagenomic Profiles (STAMP). At the family taxonomic level, there were differences in the relative abundances of the dominant taxa of bacteria that are involved in the spontaneous fermentation of millet namely Lactobacillaceae, Burkholderiaceae, Streptococcaceae, Leuconostocaceae, and Acetobacteraceae. Clostridiaceae was the dominant family in one dataset. The incidence of Lactobacillaceae and Bifidobacteriaceae suggest the probiotic characteristics of fermented millet. The datasets were collected with fermentations that were mediated by autochthonous microorganisms and the presence of some potential pathogens such as Enterobacteriaceae, Clostridiaceae, Aeromonadaceae, Microbacteiaceae, Pseudomonadaceae, and Neisseriaceae which suggest the need for standardization of fermentation approaches. The genomes show the potential to synthesize metabolites such as essential amino acids and vitamins, suggesting that the respective fermented foods can be further optimized to enhance nutritional benefits.
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Mu, Yu, Jun Huang, Rongqing Zhou, Suyi Zhang, Hui Qin, Hanlan Tang, Qianglin Pan, and Huifang Tang. "Effects of Daqu Attributes on Distribution and Assembly Patterns of Microbial Communities and Their Metabolic Function of Artificial Pit Mud." Foods 11, no. 18 (September 19, 2022): 2922. http://dx.doi.org/10.3390/foods11182922.
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Daqu provides functional microbiota and various nutrients for artificial pit mud (APM) cultivation. However, little is known about whether its attributes affect the microbiome and metabolome of APM. Here, two types of APM were manufactured by adding fortified Daqu (FD) and conventional Daqu (CD); they were comprehensively compared by polyphasic detection methods after being used for two years. The results showed that FD altered the prokaryotic communities rather than the fungal ones, resulting in increased archaea and Clostridium_sensu_stricto_12 and decreased eubacteria and Lactobacillus. Correlation analysis suggested that these variations in community structure promoted the formation of hexanoic acid, butyric acid, and the corresponding ethyl esters, whereas they inhibited that of lactic acid and ethyl lactate and thus improved the flavor quality of the APM. Notably, pH was the main driving factor for the bacterial community variation, and the total acid mediated the balance between the stochastic and the deterministic processes. Furthermore, the results of the network analysis and PICRUSt2 indicated that FD also enhanced the modularity and robustness of the co-occurrence network and the abundance of enzymes related to hexanoic acid and butyric acid production. Our study highlights the importance of Daqu attributes in APM cultivation, which are of great significance for the production of high-quality strong-flavor Baijiu.
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Muwawa, Edith M., Chinedu C. Obieze, Huxley M. Makonde, Joyce M. Jefwa, James H. P. Kahindi, and Damase P. Khasa. "16S rRNA gene amplicon-based metagenomic analysis of bacterial communities in the rhizospheres of selected mangrove species from Mida Creek and Gazi Bay, Kenya." PLOS ONE 16, no. 3 (March 23, 2021): e0248485. http://dx.doi.org/10.1371/journal.pone.0248485.
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Prokaryotic communities play key roles in biogeochemical transformation and cycling of nutrients in the productive mangrove ecosystem. In this study, the vertical distribution of rhizosphere bacteria was evaluated by profiling the bacterial diversity and community structure in the rhizospheres of four mangrove species (Sonneratia alba, Rhizophora mucronata, Ceriops tagal and Avicennia marina) from Mida Creek and Gazi Bay, Kenya, using DNA-metabarcoding. Alpha diversity was not significantly different between sites, but, significantly higher in the rhizospheres of S. alba and R. mucronata in Gazi Bay than in Mida Creek. Chemical parameters of the mangrove sediments significantly correlated inversely with alpha diversity metrics. The bacterial community structure was significantly differentiated by geographical location, mangrove species and sampling depth, however, differences in mangrove species and sediment chemical parameters explained more the variation in bacterial community structure. Proteobacteria (mainly Deltaproteobacteria and Gammaproteobacteria) was the dominant phylum while the families Desulfobacteraceae, Pirellulaceae and Syntrophobacteraceae were dominant in both study sites and across all mangrove species. Constrained redundancy analysis indicated that calcium, potassium, magnesium, electrical conductivity, pH, nitrogen, sodium, carbon and salinity contributed significantly to the species–environment relationship. Predicted functional profiling using PICRUSt2 revealed that pathways for sulfur and carbon metabolism were significantly enriched in Gazi Bay than Mida Creek. Overall, the results indicate that bacterial community composition and their potential function are influenced by mangrove species and a fluctuating influx of nutrients in the mangrove ecosystems of Gazi Bay and Mida Creek.
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Wei, Limin, Bo Zeng, Siyuan Zhang, Feng Li, Fanli Kong, Haixia Ran, Hong-Jiang Wei, Jiangchao Zhao, Mingzhou Li, and Ying Li. "Inbreeding Alters the Gut Microbiota of the Banna Minipig." Animals 10, no. 11 (November 16, 2020): 2125. http://dx.doi.org/10.3390/ani10112125.
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The gut microbiota coevolve with the host and can be stably transmitted to the offspring. Host genetics plays a crucial role in the composition and abundance of gut microbiota. Inbreeding can cause a decrease of the host’s genetic diversity and the heterozygosity. In this study, we used 16S rRNA gene sequencing to compare the differences of gut microbiota between the Diannan small-ear pig and Banna minipig inbred, aiming to understand the impact of inbreeding on the gut microbiota. Three dominant bacteria (Stenotrophlomonas, Streptococcus, and Lactobacillus) were steadily enriched in both the Diannan small-ear pig and Banna minipig inbred. After inbreeding, the gut microbiota alpha diversity and some potential probiotics (Bifidobacterium, Tricibacter, Ruminocaccae, Christensenellaceae, etc.) were significantly decreased, while the pathogenic Klebsiella bacteria was significantly increased. In addition, the predicted metagenomic analysis (PICRUSt2) indicated that several amino acid metabolisms (‘‘Valine, leucine, and isoleucine metabolism’’, ‘‘Phenylalanine, tyrosine, and tryptophan biosynthesis’’, ‘‘Histidine metabolism’’) were also markedly decreased after the inbreeding. Altogether our data reveal that host inbreeding altered the composition and the predicted function of the gut microbiome, which provides some data for the gut microbiota during inbreeding.
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Filardo, Simone, Marisa Di Pietro, Marta De Angelis, Gabriella Brandolino, Maria Grazia Porpora, and Rosa Sessa. "In-Silico Functional Metabolic Pathways Associated to Chlamydia trachomatis Genital Infection." International Journal of Molecular Sciences 23, no. 24 (December 13, 2022): 15847. http://dx.doi.org/10.3390/ijms232415847.
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The advent of high-throughput technologies, such as 16s rDNA sequencing, has significantly contributed to expanding our knowledge of the microbiota composition of the genital tract during infections such as Chlamydia trachomatis. The growing body of metagenomic data can be further exploited to provide a functional characterization of microbial communities via several powerful computational approaches. Therefore, in this study, we investigated the predicted metabolic pathways of the cervicovaginal microbiota associated with C. trachomatis genital infection in relation to the different Community State Types (CSTs), via PICRUSt2 analysis. Our results showed a more rich and diverse mix of predicted metabolic pathways in women with a CST-IV microbiota as compared to all the other CSTs, independently from infection status. C. trachomatis genital infection further modified the metabolic profiles in women with a CST-IV microbiota and was characterized by increased prevalence of the pathways for the biosynthesis of precursor metabolites and energy, biogenic amino-acids, nucleotides, and tetrahydrofolate. Overall, predicted metabolic pathways might represent the starting point for more precisely designed future metabolomic studies, aiming to investigate the actual metabolic pathways characterizing C. trachomatis genital infection in the cervicovaginal microenvironment.
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Zaytsoff, Sarah J. M., Richard R. E. Uwiera, and G. Douglas Inglis. "Physiological Stress Mediated by Corticosterone Administration Alters Intestinal Bacterial Communities and Increases the Relative Abundance of Clostridium perfringens in the Small Intestine of Chickens." Microorganisms 8, no. 10 (October 1, 2020): 1518. http://dx.doi.org/10.3390/microorganisms8101518.
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A model of physiological stress mediated by the administration of corticosterone (CORT) was used to investigate the impact of stress on the intestinal microbiota of chickens. Birds were administered CORT in their drinking water at 0, 10 (low dose CORT; LDC), and 30 (high dose CORT; HDC) mg/L. Digesta from the small intestine and ceca were examined after 1, 5, and 12 days post-initiation of CORT administration by 16S rRNA gene sequencing. A decrease in phylogenetic diversity and altered composition of bacteria were observed for HDC in the small intestine. Analysis by ANOVA-Like Differential Expression 2 (ALDEx2) showed that densities of Clostridium sensu stricto 1 bacteria were increased in the small intestine for LDC and HDC. Quantitative PCR confirmed that CORT administration increased densities of Clostridium perfringens in the small intestine, but only HDC was associated with increased densities of the bacterium in ceca. Predictive functional analysis by Phylogenetic Investigation of Communities by Reconstruction of Unobserved States 2 (PICRUSt2) showed pathways of carbohydrate metabolism to be enriched with CORT, and amino acid synthesis to be enriched in control birds in the small intestine. In conclusion, physiological stress mediated by CORT modulated bacterial communities in the small intestine and increased densities of C. perfringens. This implicates stress as an important mediator of this important enteric pathogen in poultry.
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Zhou, Dan, Ting Zhang, Long Ren, Di-an Fang, and Dongpo Xu. "Differential Study of Microbiota in the Gill and Intestine of Silver Carp (Hypophthalmichthys molitrix) from the Algae-Dominated and Hydrophyte-Dominated Areas of Taihu Lake, China." Fishes 7, no. 6 (October 25, 2022): 304. http://dx.doi.org/10.3390/fishes7060304.
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Both fish gills and guts can support lots of microbiota that play important roles in the health and growth of hosts. Although the microbiota of silver carp has been widely studied, the data on microbial variation according to fish tissues and local habitats are lacking. In this study, the microbes in the guts and gills of silver carp (Hypophthalmichthys molitrix) from the hydrophyte-dominated region (zone H) and the algae-dominated region (zone A) of Taihu Lake in autumn were analyzed. Proteobacteria, Cyanobacteria, and Firmicutes were the dominant bacteria in silver carp. The microbial diversity was higher in the gills than that in the intestines, and higher in fish from zone H than that from zone A. Beta diversity analysis revealed significant differences in microbial community structures between gill and guts, and between fish from the two habitats. Gills had a higher abundance of phyla Actinobacteria, Bacteroidetes, and Deinococcus-Thermus, and a lower abundance of verrucomicrobia than the intestine. Both tissues possessed indicator taxa, while many indicator taxa in the gill were conditional pathogens. Compared to fish from zone H, fish from zone A had more abundant Cyanobacteria, and less abundant Proteobacteria and Bacteroidetes. PICRUSt2 analysis revealed that fish microbial functions were mainly associated with metabolism, replication, repair, folding, sorting, and degradation. These results showed that the microbial community of silver carp from Taihu Lake varied according to tissues and habitats.
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Wang, Yan-Ping, Xu Liu, Chun-Yan Yi, Xing-Yu Chen, Chang-Hua Liu, Cui-Cui Zhang, Qing-Dong Chen, Song Chen, Hong-Ling Liu, and De-Qiang Pu. "The Adaptive Evolution in the Fall Armyworm Spodoptera frugiperda (Lepidoptera: Noctuidae) Revealed by the Diversity of Larval Gut Bacteria." Genes 14, no. 2 (January 26, 2023): 321. http://dx.doi.org/10.3390/genes14020321.
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Insect gut microbes have important roles in host feeding, digestion, immunity, development, and coevolution with pests. The fall armyworm, Spodoptera frugiperda (Smith, 1797), is a major migratory agricultural pest worldwide. The effects of host plant on the pest’s gut bacteria remain to be investigated to better understand their coevolution. In this study, differences in the gut bacterial communities were examined for the fifth and sixth instar larvae of S. frugiperda fed on leaves of different host plants (corn, sorghum, highland barley, and citrus). The 16S rDNA full-length amplification and sequencing method was used to determine the abundance and diversity of gut bacteria in larval intestines. The highest richness and diversity of gut bacteria were in corn-fed fifth instar larvae, whereas in sixth instar larvae, the richness and diversity were higher when larvae were fed by other crops. Firmicutes and Proteobacteria were dominant phyla in gut bacterial communities of fifth and sixth instar larvae. According to the LDA Effect Size (LEfSe) analysis, the host plants had important effects on the structure of gut bacterial communities in S. frugiperda. In the PICRUSt2 analysis, most predicted functional categories were associated with metabolism. Thus, the host plant species attacked by S. frugiperda larvae can affect their gut bacterial communities, and such changes are likely important in the adaptive evolution of S. frugiperda to host plants.
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Cayetano, Roent Dune A., Jungsu Park, Gi-Beom Kim, Ju-Hyeong Jung, and Sang-Hyoun Kim. "Enhanced anaerobic digestion of waste-activated sludge via bioaugmentation strategy—Phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt2) analysis through hydrolytic enzymes and possible linkage to system performance." Bioresource Technology 332 (July 2021): 125014. http://dx.doi.org/10.1016/j.biortech.2021.125014.
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Papale, Maria, Carmen Rizzo, Gabriella Caruso, Rosabruna La Ferla, Giovanna Maimone, Angelina Lo Giudice, Maurizio Azzaro, and Mauro Guglielmin. "First Insights into the Microbiology of Three Antarctic Briny Systems of the Northern Victoria Land." Diversity 13, no. 7 (July 15, 2021): 323. http://dx.doi.org/10.3390/d13070323.
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Different polar environments (lakes and glaciers), also in Antarctica, encapsulate brine pools characterized by a unique combination of extreme conditions, mainly in terms of high salinity and low temperature. Since 2014, we have been focusing our attention on the microbiology of brine pockets from three lakes in the Northern Victoria Land (NVL), lying in the Tarn Flat (TF) and Boulder Clay (BC) areas. The microbial communities have been analyzed for community structure by next generation sequencing, extracellular enzyme activities, metabolic potentials, and microbial abundances. In this study, we aim at reconsidering all available data to analyze the influence exerted by environmental parameters on the community composition and activities. Additionally, the prediction of metabolic functions was attempted by the phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt2) tool, highlighting that prokaryotic communities were presumably involved in methane metabolism, aromatic compound biodegradation, and organic compound (proteins, polysaccharides, and phosphates) decomposition. The analyzed cryoenvironments were different in terms of prokaryotic diversity, abundance, and retrieved metabolic pathways. By the analysis of DNA sequences, common operational taxonomic units ranged from 2.2% to 22.0%. The bacterial community was dominated by Bacteroidetes. In both BC and TF brines, sequences of the most thermally tolerant and methanogenic Archaea were detected, some of them related to hyperthermophiles.
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Lin, Yubiao, Jiejun Kong, Ling Yang, Qian He, Yan Su, Jiyue Li, Guangyu Wang, and Quan Qiu. "Soil Bacterial and Fungal Community Responses to Throughfall Reduction in a Eucalyptus Plantation in Southern China." Forests 13, no. 1 (December 31, 2021): 37. http://dx.doi.org/10.3390/f13010037.
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In subtropical plantations in southern China, how soil microbial communities respond to climate change-induced drought is poorly understood. A field experiment was conducted in a subtropical Eucalyptus plantation to determine the impacts of 50% of throughfall reduction (TR) on soil microbial community composition, function, and soil physicochemical properties. Results showed that TR reduced soil water content (SWC) and soil available phosphorus (AP) content. TR significantly altered 196 bacterial operational taxonomic units (OTUs), most of them belonging to Acidobacteria, Actinobacteria, and Proteobacteria, while there were fewer changes in fungal OTUs. At the phylum level, TR increased the relative abundance of Acidobacteria at 0–20 cm soil depth by 37.18%, but failed to influence the relative abundance of the fungal phylum. Notably, TR did not alter the alpha diversity of the bacterial and fungal communities. The redundancy analysis showed that the bacterial communities were significantly correlated with SWC, and fungal communities were significantly correlated with AP content. According to predictions of bacterial and fungal community functions using PICRUSt2 and FUNGuild platforms, TR had different effects on both bacterial and fungal communities. Overall, SWC and AP decreased during TR, resulting in greater changes in soil bacterial community structure, but did not dramatically change soil fungal community structure.
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Li, Zhenchi, Jinglin Tian, Yukun Lai, Chiu-Hong Lee, Zongwei Cai, and Chun-Fai Yu. "Puffer Fish Gut Microbiota Studies Revealed Unique Bacterial Co-Occurrence Patterns and New Insights on Tetrodotoxin Producers." Marine Drugs 18, no. 5 (May 25, 2020): 278. http://dx.doi.org/10.3390/md18050278.
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Tetrodotoxin (TTX) is a potent neurotoxin isolated mainly from toxic puffer fish. To date, the TTX biosynthetic mechanism inside its hosts remains unresolved. Here, we hypothesize the TTX synthesis relies on the host gut microbiota, including the neglected non-culturable bacteria. In these studies, we collected the gut contents from 5 puffer fish species of the genus Takifugu including one suspected hybrid species for gut microbiota study by 16S rRNA amplicon metagenomics approach. Their gut samples were divided into toxic and non-toxic groups based on the TTX concentrations in the livers detected by LC-MS/MS. Bacterial diversity studies showed that gut microbiota structures were significantly different between toxic and non-toxic species. Vibrio and Cyanobacteria centered at the gut bacterial co-occurrence network, suggesting their importance in TTX biosynthesis. The results of PICRUSt2 metagenomic prediction and gene set enrichment analysis provided new support of arginine-precursor required in TTX biosynthesis. This is the first study to profile the gut microbiota in toxic and non-toxic puffer fish species by 16S rRNA amplicon metagenomic approach, defining significant microbial co-occurrence patterns in their gut environment. Our data supported the proposed biosynthesis of TTX inside the hosts by their gut bacterial symbionts using arginine as a precursor.
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Paudel, Durga, Yasuhiro Kuramitsu, Osamu Uehara, Tetsuro Morikawa, Koki Yoshida, Sarita Giri, Syed Taufiqul Islam, et al. "Proteomic and microbiota analyses of the oral cavity during psychological stress." PLOS ONE 17, no. 5 (May 25, 2022): e0268155. http://dx.doi.org/10.1371/journal.pone.0268155.
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Psychological stress is associated with various oral diseases such as aphthous stomatitis, oral lichen planus, taste disturbances and glossodynia. However, the underlying mechanism is still unknown. The aim of this study was to determine the effect of psychological stress on salivary proteins and the oral microbiota in a rat model of chronic restraint stress. Six-week-old Sprague Dawley rats were subjected to restraint stress for four hours daily for 1 month. The behavior, weights of the adrenal glands, and serum corticosterone levels were evaluated as stress markers. Proteomic analysis of the saliva was performed using two-dimensional gel electrophoresis followed by mass spectrometry and Western blotting. Analysis of the oral microbiota was performed via 16S rRNA next-generation sequencing. The low mean body weights, lower number of entries and time spent in the open arm of elevated plus maze, high adrenal gland/body weight ratios, and high serum corticosterone levels confirmed the high levels of stress in the stress group of rats compared to the controls. Thirty-three protein spots were found to be significantly altered between the two groups. After silver staining, seven visible spots were subjected for mass spectrometry, and the expression levels of the two most significantly altered proteins, BPI fold containing family A member 2 and von Ebner’s gland protein, were confirmed by Western blotting. 16S rRNA sequencing analysis revealed a significant reduction in alpha diversity in the stress group compared to the controls. The abundances of oral bacteria, such as Facklamia and Corynebacterium, were significantly altered between the two groups. Additionally, analysis with PICRUSt2 software predicted 37 different functional pathways to be altered between the groups. In conclusion, the present study identified altered salivary proteins and oral microbiota due to psychological stress. These findings might aid in understanding the pathogenesis of stress-related oral diseases.
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Bai, Shijie, Peijun Zhang, Xianfeng Zhang, Zixin Yang, and Songhai Li. "Gut Microbial Characterization of Melon-Headed Whales (Peponocephala electra) Stranded in China." Microorganisms 10, no. 3 (March 6, 2022): 572. http://dx.doi.org/10.3390/microorganisms10030572.
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Although gut microbes are regarded as a significant component of many mammals and play a very important role, there is a paucity of knowledge around marine mammal gut microbes, which may be due to sampling difficulties. Moreover, to date, there are very few, if any, reports on the gut microbes of melon-headed whales. In this study, we opportunistically collected fecal samples from eight stranded melon-headed whales (Peponocephala electra) in China. Using high-throughput sequencing technology of partial 16S rRNA gene sequences, we demonstrate that the main taxa of melon-headed whale gut microbes are Firmicutes, Fusobacteriota, Bacteroidota, and Proteobacteria (Gamma) at the phylum taxonomic level, and Cetobacterium, Bacteroides, Clostridium sensu stricto, and Enterococcus at the genus taxonomic level. Meanwhile, molecular ecological network analysis (MENA) shows that two modules (a set of nodes that have strong interactions) constitute the gut microbial community network of melon-headed whales. Module 1 is mainly composed of Bacteroides, while Module 2 comprises Cetobacterium and Enterococcus, and the network keystone genera are Corynebacterium, Alcaligenes, Acinetobacter, and Flavobacterium. Furthermore, by predicting the functions of the gut microbial community through PICRUSt2, we found that although there are differences in the composition of the gut microbial community in different individuals, the predicted functional profiles are similar. Our study gives a preliminary inside look into the composition of the gut microbiota of stranded melon-headed whales.
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Palmieri, Orazio, Stefano Castellana, Antonio Bevilacqua, Anna Latiano, Tiziana Latiano, Anna Panza, Rosanna Fontana, et al. "Adherence to Gluten-Free Diet Restores Alpha Diversity in Celiac People but the Microbiome Composition Is Different to Healthy People." Nutrients 14, no. 12 (June 14, 2022): 2452. http://dx.doi.org/10.3390/nu14122452.
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Celiac disease (CD) is an autoimmune disease with the destruction of small intestinal villi, which occurs in genetically predisposed individuals. At the present moment, a gluten-free diet (GFD) is the only way to restore the functionality of gut mucosa. However, there is an open debate on the effects of long-term supplementation through a GFD, because some authors report an unbalance in microbial taxa composition. Methods: For microbiome analysis, fecal specimens were collected from 46 CD individuals in GFD for at least 2 years and 30 specimens from the healthy controls (HC). Data were analyzed using an ensemble of software packages: QIIME2, Coda-lasso, Clr-lasso, Selbal, PICRUSt2, ALDEx2, dissimilarity-overlap analysis, and dysbiosis detection tests. Results: The adherence to GFD restored the alpha biodiversity of the gut microbiota in celiac people but microbial composition at beta diversity resulted as different to HC. The microbial composition of the CD subjects was decreased in a number of taxa, namely Bifidobacterium longum and several belonging to Lachnospiraceae family, whereas Bacteroides genus was found to be more abundant. Predicted metabolic pathways among the CD bacterial communities revealed an important role in tetrapyrrole biosynthesis. Conclusions: CD patients in GFD had a non-dysbiotic microbial composition for the crude alpha diversity metrics. We found significant differences in beta diversity, in certain taxon, and pathways between subjects with inactive CD in GFD and controls. Collectively, our data may suggest the development of new GFD products by modulating the gut microbiota through diet, supplements of vitamins, and the addition of specific prebiotics.
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Xia, Yan, Ying Feng, Tianhua Qin, Xiaohua Zhao, Jing Lu, and Cailing Ma. "Characteristics of Vaginal Microbiome in Reproductive-Age Females with HPV Infection in Xinjiang, China." Evidence-Based Complementary and Alternative Medicine 2022 (November 1, 2022): 1–10. http://dx.doi.org/10.1155/2022/7332628.
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Objective. We investigated the characteristics of vaginal microbiome in reproductive-age females with HPV infection in Xinjiang, China. Methods. A total of 135 females of reproductive age were enrolled. There were 43 healthy HPV-negative females in control group (N group), 58 HPV-positive females in nonlesion group (P1 group), and 34 HPV-positive females in low-grade squamous intraepithelial lesion group (P2 group). DNA was extracted from the vaginal secretions, and V3–V4 regions of bacterial 16S rDNA were amplified and sequenced by NovaSeq. QIIME2 and R software were used to perform diversity analysis of bacteria. PICRUSt2 was used to predict the function of the vaginal microbiota. Results. Lactobacillus was the main genus of vaginal microbiota in asymptomatic reproductive-age females with or without HPV in Xinjiang. The diversity of vaginal microbiota in the P1 group was significantly higher than that in the N group, and the proportion of Gardnerella increased significantly. The vaginal microbiota structure of the P2 group was different from the N group, characterized by the decrease of Lactobacillus crispatus and the increase of Shuttleworthia. The function of the inordinate microbiome may play a role in accelerating HPV replication and integration. Conclusion. The structure of vaginal microbiota alters under persistent HPV infection in asymptomatic females of reproductive age in Xinjiang. The Gardnerella increase is associated with increased susceptibility to HPV infection, and Lactobacillus iners predominance and Shuttleworthia presence may be a signature of HPV infection with low-grade squamous intraepithelial lesion.
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Gao, Lei, Yin Huang, Yonghong Liu, Osama Abdalla Abdelshafy Mohamed, Xiaorong Fan, Lei Wang, Li Li, and Jinbiao Ma. "Bacterial Community Structure and Potential Microbial Coexistence Mechanism Associated with Three Halophytes Adapting to the Extremely Hypersaline Environment." Microorganisms 10, no. 6 (May 30, 2022): 1124. http://dx.doi.org/10.3390/microorganisms10061124.
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Halophytes play a crucial ecological role in drought and saline–alkali environments. However, there is limited knowledge about the structure of bacterial communities and the potential microbial coexistence mechanism associated with halophytes. This study investigated the diversity and community structure of endophytic and rhizospheric bacteria associated with three halophytes by applying high-throughput sequencing and geochemistry analyses on the studied soils. We collected 18 plant and 21 soil samples, and sequenced the V3 and V4 hypervariable regions of the 16S rRNA gene using next-generation sequencing (NGS). We also assessed geochemistry of the studied soils. The research suggested that rhizospheric bacterial richness and diversity associated with three halophytes were all significantly higher than for endophytic bacteria. The microbial community analysis indicated that Actinobacteria, Firmicutes, Bacteroidetes and Proteobacteria were the dominating bacterial phyla. Most unassigned operational taxonomic units (OTUs) implied that the microbes associated with halophytes contained abundant potential novel taxa, which are significant microbial resources. The high-abundance OTU phylogenetic tree supported the above views as well. Additionally, network analysis indicated that some conditional rare taxa (CRT) also might be keystone taxa during halophyte microbial community construction. The results of non-metric multidimensional scaling (NMDS) ordination analysis indicated significant dissimilarities in the microbial community among different sample groups. Sixty-two biomarkers were detected from seven different sample groups by linear discriminant analysis effect size (LEFSe) analysis. Microbial functions predicted based on phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt2) demonstrated that the abundances of nitrogen metabolism genes of endophytic bacteria were significantly higher than in rhizobacteria. Environmental factor analysis confirmed that different soil properties have different degrees of influence on the abundance and composition of the microbiota. To better adapt to the extreme hypersaline environment, halophytes could specifically recruit some plant beneficial bacterial taxa, such as nitrogen-fixing bacteria and extremely halophilic or halotolerant bacteria, to help them robustly grow and proliferate. All our preliminary results highlight microbial diversity and community related to halophytes grown on saline–alkali land of arid areas. Simultaneously, this work also advanced our further understanding of the halophyte microbiome associated with plants, and their role in plant adaptation to the extremely hypersaline environment.
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Tyagi, Kaomud, Inderjeet Tyagi, and Vikas Kumar. "Interspecific variation and functional traits of the gut microbiome in spiders from the wild: The largest effort so far." PLOS ONE 16, no. 7 (July 21, 2021): e0251790. http://dx.doi.org/10.1371/journal.pone.0251790.
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Spiders being one of the most diverse group in phylum arthropod are of great importance due to their role as predators, silk producer, and in medicinal applications. Spiders in prey–predator relationships play a crucial role in balancing the food-chain of any ecosystem; therefore it is essential to characterize the gut microbiota of spiders collected from natural environments. In the present work, the largest effort so far has been made to characterize the gut microbiota of 35 spider species belonging to four different families using 16S amplicon targeting sequencing. Further, we compared the gut microbiota composition including endosymbiont abundance in spider species collected from different geographical locations. The results obtained revealed the presence of genera like Acinetobacter (15%), V7clade (9%), Wolbachia (8%), Pseudomonas (5%), Bacillus (6%). Although comparative analysis revealed that the gut bacterial composition in all the spider families has a similar pattern, in terms of community richness and evenness. The bacterial diversity in the spider family, Lycosidae are more diverse than in Salticidae, Tetragnathidae and Araneidae. Furthermore, it was observed that the abundance of endosymbiont genera, i.e. Wolbachia and Rickettsia, leads to shift in the abundance of other bacterial taxa and may cause sexual alterations in spider species. Moreover, predicted functional analysis based on PICRUSt2 reveals that gut microbiota of spider species were involved in functions like metabolism of carbohydrates, cofactors and vitamins, amino acids; biosynthesis of organic compounds, fatty acids, lipids etc. Based on the results obtained, it can be said that different locations do not correlate with community composition of gut microbiota in spider species collected from natural environments.
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Zhang, Xuan, Xing Wang, Zikun Guo, Xueying Liu, Ping Wang, Xiangqun Yuan, and Yiping Li. "Antibiotic Treatment Reduced the Gut Microbiota Diversity, Prolonged the Larval Development Period and Lessened Adult Fecundity of Grapholita molesta (Lepidoptera: Tortricidae)." Insects 13, no. 9 (September 15, 2022): 838. http://dx.doi.org/10.3390/insects13090838.
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Grapholita molesta, the oriental fruit moth, is a serious pest of fruit trees with host transfer characteristics worldwide. The gut microbiota, which plays a crucial part in insect physiology and ecology, can be influenced by many elements, such as antibiotics, temperature, diet, and species. However, the effects of antibiotics on G. molesta gut microbiota are still unclear. In this study, we selected five common antibiotic agents to test the inhibition of G. molesta gut microbiota, and found ciprofloxacin shown the best antibacterial activity. After feeding 1 μg/mL of ciprofloxacin, the relative abundance of Actinobacteria and Cyanobacteria decreased significantly, while that of Firmicutes and Bacteroidetes increased. PICRUSt2 analysis indicated that most functional prediction categories were enriched in the G. molesta gut, including amino acid transport and metabolism, translation, ribosomal structure and biogenesis, carbohydrate transport and metabolism, transcription, cell wall/membrane/envelope biogenesis, and energy production and conversion. Finally, ciprofloxacin feeding significantly affected larval growth, development, and reproduction, resulting in prolonged larval development duration, shortened adult longevity, and significantly decreased single female oviposition and egg hatchability. In addition, we isolated and purified some culturable bacteria belonging to Proteobacteria, Firmicutes, Actinobacteria, and cellulase-producing bacteria from the G. molesta midgut. In brief, our results demonstrate that antibiotics can have an impact on G. molesta gut bacterial communities, which is beneficial for host growth and development, as well as helping female adults produce more fertile eggs. These results will thus provide a theoretical reference for developing new green control technology for G. molesta.
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Garibay-Valdez, Estefanía, Francesco Cicala, Marcel Martinez-Porchas, Ricardo Gómez-Reyes, Francisco Vargas-Albores, Teresa Gollas-Galván, Luis Rafael Martínez-Córdova, and Kadiya Calderón. "Longitudinal variations in the gastrointestinal microbiome of the white shrimp, Litopenaeus vannamei." PeerJ 9 (August 2, 2021): e11827. http://dx.doi.org/10.7717/peerj.11827.
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The shrimp gut is a long digestive structure that includes the Foregut (stomach), Midgut (hepatopancreas) and Hindgut (intestine). Each component has different structural, immunity and digestion roles. Given these three gut digestive tract components’ significance, we examined the bacterial compositions of the Foregut, Hindgut, and Midgut digestive fractions. Those bacterial communities’ structures were evaluated by sequencing the V3 hypervariable region of the 16S rRNA gene, while the functions were predicted by PICRUSt2 bioinformatics workflow. Also, to avoid contamination with environmental bacteria, shrimp were maintained under strictly controlled conditions. The pairwise differential abundance analysis revealed differences among digestive tract fractions. The families Rhodobacteraceae and Rubritalaceae registered higher abundances in the Foregut fraction, while in the Midgut, the families with a higher proportion were Aeromonadaceae, Beijerinckiaceae and Propionibacteriaceae. Finally, the Cellulomonadaceae family resulted in a higher proportion in the Hindgut. Regarding the predicted functions, amino acid and carbohydrate metabolism pathways were the primary functions registered for Foregut microbiota; conversely, pathways associated with the metabolism of lipids, terpenoids and polyketides, were detected in the Midgut fraction. In the Hindgut, pathways like the metabolism of cofactors and vitamins along with energy metabolism were enriched. Structural changes were followed by significant alterations in functional capabilities, suggesting that each fraction’s bacteria communities may carry out specific metabolic functions. Results indicate that white shrimp’s gut microbiota is widely related to the fraction analyzed across the digestive tract. Overall, our results suggest a role for the dominant bacteria in each digestive tract fraction, contributing with a novel insight into the bacterial community.
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Theodoro, Jaqueline Maciel Vieira, Mariana Grancieri, Mariana Juste Contin Gomes, Renata Celi Lopes Toledo, Vinícius Parzanini Brilhante de São José, Hilário Cuquetto Mantovani, Carlos Wanderlei Piler Carvalho, Bárbara Pereira da Silva, and Hércia Stampini Duarte Martino. "Germinated Millet (Pennisetum glaucum (L.) R. Br.) Flour Improved the Gut Function and Its Microbiota Composition in Rats Fed with High-Fat High-Fructose Diet." International Journal of Environmental Research and Public Health 19, no. 22 (November 18, 2022): 15217. http://dx.doi.org/10.3390/ijerph192215217.
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Germinated millet (Pennisetum glaucum (L.) R. Br.) is a source of phenolic compounds that has potential prebiotic action. This study aims at evaluating the action of germinated pearl millet on gut function and its microbiota composition in Wistar rats fed with a high-fat high-fructose (HFHF) diet. In the first stage, lasting eight weeks, the experiment consisted of two groups: AIN-93M (n = 10) and HFHF group (n = 20). In the second stage, which lasted ten weeks, the animals of the AIN-93M group (n = 10) were kept, while the HFHF group was dismembered into HFHF (HFHF diet, n = 10) and HFHF + millet (HFHF added 28.6% of germinated millet flour, n = 10) groups. After the 18th week, the urine of the animals was collected for the analysis of lactulose and mannitol intestinal permeability by urinary excretion. The histomorphometry was analyzed on the proximal colon and the fecal pH, concentration of short-chain fatty acids (SCFA), and sequencing of microbiota were performed in cecum content. The Mothur v.1.44.3 software was used for data analysis of sequencing. Alpha diversity was estimated by Chao1, Shannon, and Simpson indexes. Beta diversity was assessed by PCoA (Principal Coordinate Analysis). The functional predictive analysis was performed with PICRUSt2 software (version 2.1.2−b). Functional traits attributed to normalized OTU abundance were determined by the Kyoto Encyclopedia of Genes and Genomes (KEGG). In the results, germinated millet flour reduced Oscillibacter genus and Desulfobacterota phylum, while increasing the Eggerthellaceae family. Furthermore, germinated millet flour: increased beta diversity, cecum weight, and cecum/body weight ratio; improved gut histological parameters by increasing the depth and thickness of the crypt and the goblet cell count (p < 0.05); reduced (p < 0.05) the fecal pH and mannitol urinary excretion; increased (p < 0.05) the propionate short-chain fatty acid concentration. Thus, germinated millet has the potential to improve the composition of gut microbiota and the intestinal function of rats fed with an HFHF diet.
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Zhang, Qianqian, Zhenbing Wu, Juan Zhao, Guojie Wang, Jingwen Hao, Shuyi Wang, Yaoyao Lin, et al. "Composition and Functional Characteristics and Influencing Factors of Bacterioplankton Community in the Huangshui River, China." Microorganisms 9, no. 11 (October 29, 2021): 2260. http://dx.doi.org/10.3390/microorganisms9112260.
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Bacterial community plays a key role in environmental and ecological processes of river ecosystems. Given the special climatic and geographical conditions, studying the compositional characteristics of microorganisms in highland rivers and the relationship between such microorganisms and water physicochemical factors is important for an in-depth understanding of microbial ecological mechanisms. In the present study, high-throughput sequencing was used to investigate and study the bacterioplankton community of the Huangshui River in the ecotone zone of the Qinghai Plateau and Loess Plateau. The results showed that the Huangshui River had significantly lower alpha diversity than the plain rivers. Despite the similarity in their environmental conditions, the main taxonomic compositions of the bacterial communities were distinct between the Huangshui River and polar regions (the Arctic and Antarctica). Proteobacteria accounted for the largest proportion (30.79–99.98%) of all the sequences, followed by Firmicutes (0–49.38%). Acidiphilium was the most numerous genera, which accounted for 0.03–86.16% of the assigned 16S reads, followed by Acidocella (0–95.9%), both belonging to Alphaproteobacteria. The diverse taxa of potential pathogens, such as Acinetobacter, Pseudomonas, and Aeromonas, were also identified. A principal coordinates analysis, coupled with a canonical correspondence analysis, showed spatial variations in the bacterial community composition. The water physical properties (e.g., Cr6+, total phosphorus, and CODMn); altitude; and land use (e.g., urban land cover and aquaculture) determined the distribution of the bacterioplankton composition. PICRUSt2 revealed that the overall functional profiles of the bacterial communities in different samples were similar, and our results suggested the potential health risks of water sources in this area. This work provided valuable insight into the composition of the plankton bacterial community and its relationship with the environmental factors in the Huangshui River in the ecotone zone of the Qinghai Plateau and Loess Plateau and a theoretical foundation for ecological health management.
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Wang, Q., S. X. Zhang, J. Qiao, G. Shi, R. Zhao, S. Song, Y. Zhang, Q. Yu, X. LI, and P. F. He. "AB0824 ANALYSIS OF GUT MICROBIOTA IN RHEUMATOID ARTHRITIS PATIENTS." Annals of the Rheumatic Diseases 80, Suppl 1 (May 19, 2021): 1436.1–1436. http://dx.doi.org/10.1136/annrheumdis-2021-eular.1944.
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Background:Gastrointestinal microbiota, particularly gut microbiota is an indispensable environmental factor in the progression of Rheumatoid Arthritis (RA). Understanding the diversity and function of the intestinal flora in patients with RA is part and parcel to understand the relationship between microbiota and human health.Objectives:This study aimed to identify the diversity and function of the intestinal flora in patients with RA.Methods:A total of 166 participants were recruited in this study, comprising 93 RA patients and 73 age and sex-matched healthy controls (HCs). Microbial genome was extracted from approximately 250mg fresh fecal samples from all participants using QIAamp PowerFecal DNA Kit (Qiagen). The V3-V4 variable regions of bacterial 16S rRNA genes were sequenced with the Illumina Miseq PE300 system. Sequence data were compiled and processed using Qiime2. Sequences were grouped into operational taxonomic units (ASVs)1. Microbial diversity was estimated by the Simpson index. PICRUSt2 was used to predict KEGG functional pathway differences between RA and HC intestinal flora functions based on ASV Tables2. Linear Discriminant Analysis (LDA) Effect Size (LEfSe) analysis was performed using LEfSe software to discovery the different intestinal flora and functions between RA and healthy.Results:The alpha-diversity index of Simpson the microbiome in RA patients was lower than that of HCs (Figure 1a, P <0.05). Compared with HCs, bacterial Bacilli and Lactobacillales were more abundant in patients with RA (Figure 1b, P <0.05). In contrast, Marinifilaceae, Peptococcaceae, Peptococcales and Phascolarcto bacterium were less abundant in the RA group (Figure 1b, P <0.05). As shown in Figure 1c, propanoate metabolism, taurine and hypotaurine metabolism, ascorbate and aldarate metabolism, biosynthesis of siderophore group nonribosomal peptides and glutathione metabolism were the most significantly altered pathways in RA (P <0.05). Epithelial cell signaling in Helicobacter pylori infection, RNA transport, RNA degradation and plant-pathogen interaction were the most significantly altered pathways in HC (P <0.05). The different KEGG metabolic pathways were mainly concentrated in carbohydrate and amino acid metabolism.Conclusion:Gut dysbiosis in RA patients mainly characterized by reduced the diversity and impaired abundance of the intestinal flora, which severely influence the metabolism of gastrointestinal microbiota. The discovery of the associated intestinal microbiota of RA may provide a new idea for RA treatment.References:[1]Han L, Zhao K, Li Y, et al. A gut microbiota score predicting acute graft-versus-host disease following myeloablative allogeneic hematopoietic stem cell transplantation. Am J Transplant 2020;20(4):1014-27. doi: 10.1111/ajt.15654 [published Online First: 2019/10/13][2]Liss MA, White JR, Goros M, et al. Metabolic Biosynthesis Pathways Identified from Fecal Microbiome Associated with Prostate Cancer. Eur Urol 2018;74(5):575-82. doi: 10.1016/j.eururo.2018.06.033 [published Online First: 2018/07/17]Acknowledgements:This project was supported by National Science Foundation of China (82001740), Open Fund from the Key Laboratory of Cellular Physiology (Shanxi Medical University) (KLCP2019) and Innovation Plan for Postgraduate Education in Shanxi Province (2020BY078).Disclosure of Interests:None declared
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Weinert, Jennifer R., Amy S. Biddle, and Carey A. Williams. "PSIV-17 Impacts of high forage crude protein concentrations on the equine fecal microbiome." Journal of Animal Science 99, Supplement_3 (October 8, 2021): 297. http://dx.doi.org/10.1093/jas/skab235.546.
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Abstract The objective of this study was to evaluate effects of forage crude protein (CP) concentrations on the equine fecal microbiome. Six mares were assigned to either a high-protein (HP; 24% CP) or normal-protein (NP; 15% CP) hay cube diet in a randomized cross-over design. Fecal samples were collected on the last day of each 35-d period. Branched-chain and short-chain fatty acids (SCFA) were measured by GC-MS; data were analyzed by mixed model ANOVA in R. 16S rRNA gene sequence analysis was conducted in Qiime2. Alpha and beta diversity were assessed by Kruskall-Wallis Tests and PERMANOVA. Taxonomy was assigned using SILVA. Metacyc pathways were predicted with PICRUSt2. Differential genus-level and pathway abundances were analyzed by LefSe (LDA >2.0). Significance was set at p≤0.05. Species richness did not differ by diet, but evenness was greater in NP vs. HP. Beta diversity metrics including Weighted UniFrac also differed by diet. Genera including Methanocorpusculum, Rikenellaceae RC9 gut group, and Eubacterium coprostanoligenes group were more abundant in HP. Treponema and Fibrobacters were more abundant in NP. Twenty pathways related to amino acid synthesis were identified as markers of NP, while 10 pathways related to amino acid degradation and SCFA synthesis were markers of HP. Pathway predictions were supported by metabolite analyses, with acetate (HP: 751; LP: 632 ± 49 ug/g), propionate (HP: 565; NP: 421 ± 43 ug/g), butyrate (HP: 341; LP: 210 ± 34 ug/g), and valerate (HP: 80; NP: 42 ± 11 ug/g) greater in HP than NP. Isobutyrate (HP: 108; NP: 94 ± 7 ug/g; P = 0.09), and isovalerate (HP: 91; NP: 48 ± 10 ug/g) were also greater in HP. These results demonstrate that consuming higher-CP forages impacts equine hindgut microbiota structure and function, leading to increased rates of protein fermentation. Further research is needed to determine physiological significance in forage-fed horses.
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Zhong, Rong, Zhaolan Zi, Peiru Wang, Hafeez Noor, Aixia Ren, Yongkang Ren, Min Sun, and Zhiqiang Gao. "Effects of Five Consecutive Years of Fallow Tillage on Soil Microbial Community Structure and Winter Wheat Yield." Agronomy 13, no. 1 (January 11, 2023): 224. http://dx.doi.org/10.3390/agronomy13010224.
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To evaluate the effects of long-term fallow tillage on soil microbial community structure in different soil layers and winter wheat yield, we conducted a 5-year long-term field experiment in the Loess Plateau, China, using three fallow tillage methods: no-tillage (NT), subsoiling tillage (ST), and deep plowing (DP). The soil physical and chemical properties, community structure, and composition of soil bacteria and fungi in the 0–20 cm and 20–40 cm soil layers, and winter wheat yield were analyzed. The results showed that, compared with DP, NT and ST significantly increased soil moisture content (SWC), soil organic carbon (SOC) content, and dissolved organic carbon (DOC) contents in 0–20 cm soil layer (p < 0.05), and significantly increased soil microbial community Shannon and Simpson index in 0–40 cm soil layer (p < 0.05). Compared with NT, ST and DP significantly increased SWC and SOC contents in 20–40 cm soil layer (p < 0.05). Actinobacteria and Ascomycota were the most abundant bacteria and fungi in the soil of the experimental site. Redundancy analysis further showed that soil physicochemical properties (SWC, SOC, DOC, and DON) were closely related to the microbial community. PICRUSt2 prediction results showed that DP increased the metabolic functional diversity of bacteria and fungi. ST and DP significantly increased the yield of winter wheat, and DP had the best effect. In conclusion, subsoiling tillage and deep plowing were beneficial to the accumulation and utilization of natural precipitation and the improvement of soil microbial community structure. Deep plowing was beneficial to the decomposition and metabolism of straw and organic fertilizer, and improved the catabolic ability of microbial community, thus increasing the yield of winter wheat.
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Wu, Zhenbing, Qianqian Zhang, Yaoyao Lin, Jingwen Hao, Shuyi Wang, Jingyong Zhang, and Aihua Li. "Taxonomic and Functional Characteristics of the Gill and Gastrointestinal Microbiota and Its Correlation with Intestinal Metabolites in NEW GIFT Strain of Farmed Adult Nile Tilapia (Oreochromis niloticus)." Microorganisms 9, no. 3 (March 17, 2021): 617. http://dx.doi.org/10.3390/microorganisms9030617.
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The gill and gastrointestinal tract are primary entry routes for pathogens. The symbiotic microbiota are essential to the health, nutrition and disease of fish. Though the intestinal microbiota of Nile tilapia (Oreochromis niloticus) has been extensively studied, information on the mucosa-associated microbiota of this species, especially the gill and gastrointestinal mucosa-associated microbiota, is lacking. This study aimed to characterize the gill and gastrointestinal mucosa- and digesta-associated microbiota, as well as the intestinal metabolite profiles in the New Genetically Improved Farmed Tilapia (NEW GIFT) strain of farmed adult Nile tilapia by high-throughput sequencing and gas chromatography/mass spectrometry metabolomics. The diversity, structure, composition, and predicted function of gastrointestinal microbiota were significantly different across gastrointestinal regions and sample types (Welch t-test; p < 0.05). By comparing the mucosa- and digesta-associated microbiota, linear discriminant analysis (LDA) effect size (LEfSe) analysis revealed that Pelomonas, Ralstoniapickettii, Comamonadaceae, and Staphylococcus were significantly enriched in the mucosa-associated microbiota, whereas many bacterial taxa were significantly enriched in the digesta-associated microbiota, including Chitinophagaceae, Cetobacterium, CandidatusCompetibacter, Methyloparacoccus, and chloroplast (LDA score > 3.5). Furthermore, Undibacterium, Escherichia-Shigella, Paeniclostridium, and Cetobacterium were dominant in the intestinal contents and mucosae, whereas Sphingomonasaquatilis and Roseomonasgilardii were commonly found in the gill and stomach mucosae. The Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt2) analysis revealed that the predictive function of digesta-associated microbiota significantly differed from that of mucosa-associated microbiota (R = 0.8152, p = 0.0001). In addition, our results showed a significant interdependence between specific intestinal microbes and metabolites. Notably, the relative abundance values of several potentially beneficial microbes, including Undibacterium, Crenothrix, and Cetobacterium, were positively correlated with most intestinal metabolites, whereas the relative abundance values of some potential opportunistic pathogens, including Acinetobacter, Mycobacterium, Escherichia-Shigella, Paeniclostridium, Aeromonas, and Clostridiumsensustricto 1, were negatively correlated with most intestinal metabolites. This study revealed the characteristics of gill and gastrointestinal mucosa-associated and digesta-associated microbiota of farmed Nile tilapia and identified a close correlation between intestinal microbes and metabolites. The results serve as a basis for the effective application of targeted probiotics or prebiotics in the diet to regulate the nutrition and health of farmed tilapia.
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Elmassry, Moamen, Rui Wang, Abdul Hamood, Volker Neugebauer, and Chwan-Li Shen. "Two Isomers of Ginger Root Extracts Modify Composition and Function of Gut Microbiota in Rats Treated with Neuropathic Pain." Current Developments in Nutrition 4, Supplement_2 (May 29, 2020): 394. http://dx.doi.org/10.1093/cdn/nzaa045_027.
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Abstract Objectives Emerging evidence has suggested that gut microbiota plays a key role during the development of chronic pain, such as neuropathic pain (NP). This study was to evaluate the effects of two ginger root extract isomers (gingerols and shogaols) on the composition and function of gut microbiota in animals with NP. Methods Sixteen male Sprague-Dawley rats were randomly assigned into 4 groups: sham group, spinal nerve ligation (SNL) group as the pain control group, SNL + gingerols-enriched ginger (GEG) extract group, and SNL + shogaols-enriched ginger (SEG) extract group. Animals in GEG and SEG groups were fed their respective diets on the day of SNL surgery for 30 days. At day 30, fecal samples were collected for microbiota composition and functional analyses. 16S rRNA gene sequencing was conducted from fecal samples and microbiome data analysis was performed with QIIME2 and PICRUSt2. Data were analyzed using non-parametric Kruskal–Wallis test to compare GEG and SEG with SNL group. Results Based on the results of alpha-diversity analyses, neither GEG nor SEG treatment affected the evenness of microbiome. Gingerols or shogaols supplementation into the diet reduced the richness of the gut microbiome, compared to the SNL group. Relative to the SNL group, GEG group had an increase in the relative abundance of the genus Faecalitalea, while SEG group had an increase in the relative abundance of the genus Aerococcus and species Bacteroides massiliensis. In comparison to SNL group, both GEG and SEG groups showed a decrease in the relative abundance of the family Muribaculaceae and the genus Rikenellaceae RC9 gut group. Functional profiling results revealed that relative to the SNL group, both GEG and SEG supplementation increased the proportion of biosynthetic pathways related to energy metabolism (i.e., pentose phosphate pathway and sugar degradation) and peptidoglycan biosynthesis. Furthermore, GEG and SEG differentially modified amino acid-related metabolic pathways, i.e., tyrosine degradation, tryptophan biosynthesis, arginine, and ornithine biosynthesis. Conclusions GEG and SEG exhibited differential effects on the microbiome composition and function, suggesting a prebiotic potential for dietary ginger root intake in the management of NP. Funding Sources Texas Tech University Health Sciences Center.
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Libertucci, J., M. Constante, H. J. Galipeau, J. C. Szamosi, G. H. Rueda, M. I. Pinto-Sanchez, C. M. Southward, et al. "A46 BIOGEOGRAPHIC VARIATION AND FUNCTIONAL PATHWAYS OF THE GUT MICROBIOTA IN CELIAC DISEASE." Journal of the Canadian Association of Gastroenterology 5, Supplement_1 (February 21, 2022): 53–54. http://dx.doi.org/10.1093/jcag/gwab049.045.
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Abstract Background Genes and gluten are necessary, but insufficient to cause celiac disease (CeD), as risk alleles (DQ2 or DQ8) are prevalent in ~30–40% of the healthy population consuming gluten. Gut microbiota shifts and infections have been proposed as risk modulators. Biogeographic characterization of the microbiota in CeD patients and its functional significance are limited, particularly at the duodenum, the main site of inflammation. Aims We studied microbiota composition and predicted function along the gastrointestinal tract and investigated the impact of host genetics and CeD activity. Methods We used 16S rRNA gene sequencing (Illumina) and predicted gene function analysis (PICRUSt2), to study the microbiota in duodenal biopsies (D1, D2 and D3), duodenal aspirates, and fecal samples from patients with active CeD (n= 24) (biopsy and serology confirmed) and controls (non-celiac, n= 41). CeD alleles were determined in consented participants using DQ-CD typing. Small intestinal samples from controls (DQ2-/- = 14; DQ2+/- = 7) and CeD (DQ2+/- = 12) were used for further analysis and to colonize C57BL/6 germ-free mice for gluten metabolism studies. Results Microbiota community composition and predicted function was mainly determined by intestinal location (P= 0.001). Within the duodenum, but not in stool, CeD patients had increased abundance of opportunistic pathogens. Escherichia coli was increased in D1, Streptococcus pneumoniae in D2, and Neisseria in D3 versus controls. Predicted bacterial protease and peptidase genes were altered in CeD DQ2+/- patients versus DQ2-/- controls. In DQ2+/- controls, fewer predicted bacterial genes were altered compared to CeD DQ2+/- patients. Impaired capacity to metabolize gluten was confirmed in germ-free mice colonized with microbiota from CeD (DQ2+/-), but not DQ2+/- or DQ2-/- controls. Conclusions In the duodenum, CeD is associated with increased opportunistic pathogens and altered bacterial proteolytic profile. These are not determined by genetic predisposition, as CeD and controls with similar genetic background differed in its predicted bacterial proteolytic function, which was confirmed in mice colonized with duodenal microbiota using these cohorts. Our study highlights the need for defining sampling location in studies investigating the role of microbiota in CeD. Funding Agencies CAG, CCC, CIHR
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Wu, Xuangao, Tatsuya Unno, Suna Kang, and Sunmin Park. "A Korean-Style Balanced Diet Has a Potential Connection with Ruminococcaceae Enterotype and Reduction of Metabolic Syndrome Incidence in Korean Adults." Nutrients 13, no. 2 (February 3, 2021): 495. http://dx.doi.org/10.3390/nu13020495.
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Metabolic syndrome is associated with usual dietary patterns that may be involved in enterotypes. We aimed to understand the potential relationship of enterotypes and dietary patterns to influence metabolic syndrome in the Koreans. Using the Korea National Health and Nutrition Examination Survey (KNHANES)-VI in 2014, metabolic parameters were also analyzed among the dietary patterns classified by principal component analysis in Korean adults. The fecal microbiota data of 1199 Korean adults collected in 2014 were obtained from the Korea Centers for Disease Control and Prevention. Enterotypes were classified based on Dirichlet multinomial mixtures (DMM) by Mothur v.1.36. The functional abundance of fecal bacteria was analyzed using the PICRUSt2 pipeline. Korean adults were clustered into three dietary patterns including Korean-style balanced diets (KBD, 20.4%), rice-based diets (RBD, 17.2%), and Western-style diets (WSD, 62.4%) in KNHANES. The incidence of metabolic syndrome was lowered in the order of RBD, WSD, and KBD. The participants having a KBD had lower serum C-reactive protein and triglyceride concentrations than those with RBD and WSD (p < 0.05). Three types of fecal bacteria were classified as Ruminococcaceae type (ET-R, 28.7%), Prevotella type (ET-P, 52.2%), and Bacteroides type (ET-B, 42.1%; p < 0.05). ET-P had a higher abundance of Prevotella copri, while ET-R contained a higher abundance of Alistipes, Akkermansia muciniphila, Bifidobacterium adolescentis, and Faecalibacterium prausnitzii. ET-B had a higher abundance of the order Bilophila (p < 0.05). Metabolism of propanoate, starch, and sucrose in fecal microbiome was higher in ET-P and ET-R, whereas fatty acid metabolism was enhanced in ET-B. Fecal microbiota in ET-P and ET-B had higher lipopolysaccharide biosynthesis activity than that in ET-R. The metabolic results of KBD and RBD were consistent with ET-R and ET-P’s gut microbiota metabolism, respectively. In conclusion, Korean enterotypes of ET-P, ET-B, and ET-R were associated with RBD, WSD, and KBD, respectively. This study suggests a potential link between dietary patterns, metabolic syndrome, and enterotypes among Korean adults.
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Ma, Yaling, Hucheng Wang, Chunjie Li, and Kamran Malik. "The Potential Use of Endophyte-Free inebrians as Sheep Feed Evaluated with In Vitro Fermentation." Fermentation 8, no. 9 (August 24, 2022): 419. http://dx.doi.org/10.3390/fermentation8090419.
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Endophytic fungal infection is the major reason for intoxication of animals caused by drunken horse grass. Fortunately, it has been established that seed detoxification techniques and isolation of endophytic fungi infect non-endophytic fungi populations with the same genetic background as endophyte-infected Achnatherum inebrians. Moreover, sheep can use endophyte-free Achnatherum inebriants (EF) without obvious toxicity symptoms. The present study selected EF as a representative grass, consisting of five different replacement levels, EF0, EF25, EF50, EF75, and EF100, corresponding to 0%, 25%, 50%, 75%, and 100% of the fermentation substrate, respectively. Simultaneously, in vitro fermentation and the 16S rRNA amplicon sequencing method was used to explore the effect of EF on sheep ruminal fermentation and microbial diversity. The results revealed that EF100 had the highest values for pH, acetate: propionate, the Patescibacteria, Kiritimatiellaeota, and Synergistetes phylum levels, Ruminococcaceae, Prevotellaceae, and Saccharofermentans genus levels than the other treatments (p < 0.05). In contrast, EF25 was associated with higher levels of abundance-based coverage estimator (ACE), Chaol index of the phyla Synergistetes and Bacteroidetes, and of the genus Erysipelotrichaceae, Rikenellaceae, and Prevotella as compared with other treatments (p < 0.05). EF50 resulted in the greatest values for the genus Christensenellaceae and Lachnospiraceae as compared with other treatments (p < 0.05). EF75 resulted in the greatest values for the Shannon index as compared with other treatments (p < 0.05). EF0 resulted in the greatest values for gas production (GP), ammonia nitrogen (NH3-N), total volatile fatty acid (TVFA), acetate, propionate, butyrate, valerate, isobutyrate, isovalerate, and the phyla Firmicutes, Proteobacteria, and Spirochaetes, and the genus Succiniclasticum, Ruminobacter, Family_XIII and Treponema as compared with other treatments (p < 0.05). PICRUSt2 analysis indicated that most of the functional prediction pathways were involved in Carbohydrate metabolism and, Amino acid metabolism. Therefore, the recommended ratio of EF in sheep diet should range from 25% to 50%, and the maximum proportion should not exceed 75%.
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Wang, Siran, Yuxin Wang, Haopeng Liu, Xinbao Li, Jie Zhao, Zhihao Dong, Junfeng Li, Niaz Ali Kaka, Mudasir Nazar, and Tao Shao. "Using PICRUSt2 to explore the functional potential of bacterial community in alfalfa silage harvested at different growth stages." Chemical and Biological Technologies in Agriculture 9, no. 1 (December 19, 2022). http://dx.doi.org/10.1186/s40538-022-00372-6.
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Abstract Background This study evaluated the effects of growth stage and storage time on fermentation characteristics, bacterial communities and their functionality in alfalfa (Medicago sativa L.) silage. Alfalfa was harvested at initial flowering (10–20% bloom, AL1) and full flowering (> 80% bloom, AL2) stages, respectively. The harvested alfalfa was ensiled in 15 L plastic silos. Triplicate silos were sampled after 1, 3, 7, 15, 30 and 60 days of ensiling, respectively. Fermentation products were analyzed on each sampling day. The bacterial communities and their functional potential after 3 and 60 days were analyzed by high-throughput sequencing technique and PICRUSt2 method. Results AL2 had better fermentation quality than AL1 with lower pH, ammonia nitrogen and butyric acid concentrations and higher lactic acid concentrations on day 60. AL2 had higher abundances of Weissella and Lactobacillus after 3 days, and lower abundances of Enterobacter and Enterobacteriaceae on day 60 compared to AL1. In metabolic pathway analysis, ensiling promoted the carbohydrate and amino acid metabolism, and inhibited the signal transduction and membrane transport. In enzyme analysis, AL2 had lower abundances of nitrite reductase (NADH) and ornithine decarboxylase than AL1 on day 60. In phenotype analysis, AL2 had higher proportions of facultatively anaerobic and lower proportions of anaerobic, potentially pathogenic and gram negative than AL1 on day 60. Conclusions High throughput sequencing technique combined with PICRUSt2 can be successfully used to describe the changes of bacterial communities and their functionality in silage. This approach can improve our understanding of the silage microbiology to further regulate the fermentation products. Graphical Abstract
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Pérez-Losada, Marcos, Dhatri Badri Narayanan, Allison R. Kolbe, Ignacio Ramos-Tapia, Eduardo Castro-Nallar, Keith A. Crandall, and Jorge Domínguez. "Comparative Analysis of Metagenomics and Metataxonomics for the Characterization of Vermicompost Microbiomes." Frontiers in Microbiology 13 (May 10, 2022). http://dx.doi.org/10.3389/fmicb.2022.854423.
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The study of microbial communities or microbiotas in animals and environments is important because of their impact in a broad range of industrial applications, diseases and ecological roles. High throughput sequencing (HTS) is the best strategy to characterize microbial composition and function. Microbial profiles can be obtained either by shotgun sequencing of genomes, or through amplicon sequencing of target genes (e.g., 16S rRNA for bacteria and ITS for fungi). Here, we compared both HTS approaches at assessing taxonomic and functional diversity of bacterial and fungal communities during vermicomposting of white grape marc. We applied specific HTS workflows to the same 12 microcosms, with and without earthworms, sampled at two distinct phases of the vermicomposting process occurring at 21 and 63 days. Metataxonomic profiles were inferred in DADA2, with bacterial metabolic pathways predicted via PICRUSt2. Metagenomic taxonomic profiles were inferred in PathoScope, while bacterial functional profiles were inferred in Humann2. Microbial profiles inferred by metagenomics and metataxonomics showed similarities and differences in composition, structure, and metabolic function at different taxonomic levels. Microbial composition and abundance estimated by both HTS approaches agreed reasonably well at the phylum level, but larger discrepancies were observed at lower taxonomic ranks. Shotgun HTS identified ~1.8 times more bacterial genera than 16S rRNA HTS, while ITS HTS identified two times more fungal genera than shotgun HTS. This is mainly a consequence of the difference in resolution and reference richness between amplicon and genome sequencing approaches and databases, respectively. Our study also revealed great differences and even opposite trends in alpha- and beta-diversity between amplicon and shotgun HTS. Interestingly, amplicon PICRUSt2-imputed functional repertoires overlapped ~50% with shotgun Humann2 profiles. Finally, both approaches indicated that although bacteria and fungi are the main drivers of biochemical decomposition, earthworms also play a key role in plant vermicomposting. In summary, our study highlights the strengths and weaknesses of metagenomics and metataxonomics and provides new insights on the vermicomposting of white grape marc. Since both approaches may target different biological aspects of the communities, combining them will provide a better understanding of the microbiotas under study.
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Inukai, Yosuke, Kenta Yamamoto, Takashi Honda, Takanori Ito, Norihiro Imai, Yoji Ishizu, Masanao Nakamura, Hiroki Kawashima, and Masatoshi Ishigami. "Differences in the intestinal microbiome associated with diarrhea during lenvatinib treatment for hepatocellular carcinoma." Digestive Diseases, March 28, 2022. http://dx.doi.org/10.1159/000524298.
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Introduction: Lenvatinib has been widely used for the treatment of advanced hepatocellular carcinoma (HCC). Some adverse events, including diarrhea, have been reported for lenvatinib. Diarrhea may be associated with the changes in the intestinal microbiome; however, the underlying mechanism have not been elucidated. Aim: In this study, we aimed to investigate the relationship between the intestinal microbiome and diarrhea caused by lenvatinib via analysis of fecal samples collected before treatment. Methods: A total of 21 patients with advanced HCC who were treated with lenvatinib were enrolled. Fecal samples were collected from patients. The patients were divided into diarrhea (n=8) and non-diarrhea groups (n=12). We compared the characteristics of patients, incidence of adverse events, composition of the intestinal microbiome, and enrichment of functional pathways between both groups using QIIME2 and PICRUSt2. Results: The median age of the two groups was 73 years. The non-diarrhea group comprised a relatively higher number of male patients than the diarrhea group however, there were no significant differences in patient characteristics between both groups. The proportion of the microbiome was similar, and alpha and beta diversities were not significantly different between both groups. The relative abundance of order Bacteroidales, including Parabacteroides and Prevotella, was higher in the diarrhea group than in the non-diarrhea group. PICRUSt2 analysis showed some metabolic pathways, including butanoate (butyrate) metabolism, were enriched in the non-diarrhea group when compared with those in the diarrhea group. Conclusion: Differences in the intestinal microbiomes and their functions may influence the incidence of diarrhea during lenvatinib treatment.
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Hu, Xiaomin, Yue Fan, Hanyu Li, Ruilin Zhou, Xinyue Zhao, Yueshen Sun, and Shuyang Zhang. "Impacts of Cigarette Smoking Status on Metabolomic and Gut Microbiota Profile in Male Patients With Coronary Artery Disease: A Multi-Omics Study." Frontiers in Cardiovascular Medicine 8 (October 28, 2021). http://dx.doi.org/10.3389/fcvm.2021.766739.
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Background: Cigarette smoking has been considered a modifiable risk factor for coronary artery disease (CAD). Changes in gut microbiota and microbe-derived metabolites have been shown to influence atherosclerotic pathogenesis. However, the effect of cigarette smoking on the gut microbiome and serum metabolites in CAD remains unclear.Method: We profiled the gut microbiota and serum metabolites of 113 male participants with diagnosed CAD including 46 current smokers, 34 former smokers, and 33 never smokers by 16S ribosomal RNA (rRNA) gene sequencing and untargeted metabolomics study. A follow-up study was conducted. PICRUSt2 was used for metagenomic functional prediction of important bacterial taxa.Results: In the analysis of the microbial composition, the current smokers were characterized with depleted Bifidobacterium catenulatum, Akkermansia muciniphila, and enriched Enterococcus faecium, Haemophilus parainfluenzae compared with the former and never smokers. In the untargeted serum metabolomic study, we observed and annotated 304 discriminant metabolites, uniquely including ceramides, acyl carnitines, and glycerophospholipids. Pathway analysis revealed a significantly changed sphingolipids metabolism related to cigarette smoking. However, the change of the majority of the discriminant metabolites is possibly reversible after smoking cessation. While performing PICRUSt2 metagenomic prediction, several key enzymes (wbpA, nadM) were identified to possibly explain the cross talk between gut microbiota and metabolomic changes associated with smoking. Moreover, the multi-omics analysis revealed that specific changes in bacterial taxa were associated with disease severity or outcomes by mediating metabolites such as glycerophospholipids.Conclusions: Our results indicated that both the gut microbiota composition and metabolomic profile of current smokers are different from that of never smokers. The present study may provide new insights into understanding the heterogenic influences of cigarette smoking on atherosclerotic pathogenesis by modulating gut microbiota as well as circulating metabolites.
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Chen, Jiung-Wen, Jer-Horng Wu, Wei-Fan Chiang, Yuh-Ling Chen, Wei-Sheng Wu, and Li-Wha Wu. "Taxonomic and Functional Dysregulation in Salivary Microbiomes During Oral Carcinogenesis." Frontiers in Cellular and Infection Microbiology 11 (September 16, 2021). http://dx.doi.org/10.3389/fcimb.2021.663068.
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Exploring microbial community compositions in humans with healthy versus diseased states is crucial to understand the microbe-host interplay associated with the disease progression. Although the relationship between oral cancer and microbiome was previously established, it remained controversial, and yet the ecological characteristics and their responses to oral carcinogenesis have not been well studied. Here, using the bacterial 16S rRNA gene amplicon sequencing along with the in silico function analysis by PICRUSt2 (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States 2), we systematically characterized the compositions and the ecological drivers of saliva microbiome in the cohorts of orally healthy, non-recurrent oral verrucous hyperplasia (a pre-cancer lesion), and oral verrucous hyperplasia–associated oral cancer at taxonomic and function levels, and compared them with the re-analysis of publicly available datasets. Diversity analyses showed that microbiome dysbiosis in saliva was significantly linked to oral health status. As oral health deteriorated, the number of core species declined, and metabolic pathways predicted by PICRUSt2 were dysregulated. Partitioned beta-diversity revealed an extremely high species turnover but low function turnover. Functional beta-diversity in saliva microbiome shifted from turnover to nestedness during oral carcinogenesis, which was not observed at taxonomic levels. Correspondingly, the quantitative analysis of stochasticity ratios showed that drivers of microbial composition and functional gene content of saliva microbiomes were primarily governed by the stochastic processes, yet the driver of functional gene content shifted toward deterministic processes as oral cancer developed. Re-analysis of publicly accessible datasets supported not only the distinctive family taxa of Veillonellaceae and Actinomycetaceae present in normal cohorts but also that Flavobacteriaceae and Peptostreptococcaceae as well as the dysregulated metabolic pathways of nucleotides, amino acids, fatty acids, and cell structure were related to oral cancer. Using predicted functional profiles to elucidate the correlations to the oral health status shows superior performance than using taxonomic data among different studies. These findings advance our understanding of the oral ecosystem in relation to oral carcinogenesis and provide a new direction to the development of microbiome-based tools to study the interplay of the oral microbiome, metabolites, and host health.
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Veses, Verónica, Pedro González-Torres, Belén Carbonetto, Mª del Mar Jovani-Sancho, Raquel González-Martínez, Isidoro Cortell-Ballester, and Chirag C. Sheth. "Dental black plaque: metagenomic characterization and comparative analysis with white-plaque." Scientific Reports 10, no. 1 (September 29, 2020). http://dx.doi.org/10.1038/s41598-020-72460-2.
Full textAbstract:
Abstract Extrinsic black dental staining is an external dental discoloration of bacterial origin, considered a special form of dental plaque. Currently, there is no definitive therapeutic option for eliminating black stain. This study employed 16S rRNA metagenomics to analyze black stain and white-plaque samples from 27 adult volunteers. Study objectives were to: describe the microbial diversity of adult black stain samples; characterize their taxonomic profile; compare the microbiomes of black stain versus white-plaque from adult volunteers and propose a functional map of the black stain microbiome using PICRUSt2. The black stain microbiome was poorer in species diversity as compared to white-plaque. The five most abundant genera in black stain were Capnocytophaga, Leptotrichia, Fusobacterium, Corynebacterium and Streptococcus. Functional analysis of microbial species revealed conserved and consistent clustering of functional pathways within and between black stain and white-plaque microbiomes. We describe enrichment of heme biosynthetic pathways in black stain. Our results suggest that the dysbiosis in black stain resembles “orally healthy” communities. The increased abundance of heme biosynthetic pathways suggests that heme-dependent iron sequestration and subsequent metabolism are key for black stain formation. Further research should decipher the regulation of heme biosynthetic genes and characterize the temporal sequence leading to colonization and dysbiosis.
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Darwish, Nadia, Jonathan Shao, Lori L. Schreier, and Monika Proszkowiec-Weglarz. "Choice of 16S ribosomal RNA primers affects the microbiome analysis in chicken ceca." Scientific Reports 11, no. 1 (June 4, 2021). http://dx.doi.org/10.1038/s41598-021-91387-w.
Full textAbstract:
AbstractWe evaluated the effect of applying different sets of 16S rRNA primers on bacterial composition, diversity, and predicted function in chicken ceca. Cecal contents from Ross 708 birds at 1, 3, and 5 weeks of age were collected for DNA isolation. Eight different primer pairs targeting different variable regions of the 16S rRNA gene were employed. DNA sequences were analyzed using open-source platform QIIME2 and the Greengenes database. PICRUSt2 was used to determine the predicted function of bacterial communities. Changes in bacterial relative abundance due to 16S primers were determined by GLMs. The average PCR amplicon size ranged from 315 bp (V3) to 769 bp (V4–V6). Alpha- and beta-diversity, taxonomic composition, and predicted functions were significantly affected by the primer choice. Beta diversity analysis based on Unweighted UniFrac distance matrix showed separation of microbiota with four different clusters of bacterial communities. Based on the alpha- and beta-diversity and taxonomic composition, variable regions V1–V3(1) and (2), and V3–V4 and V3–V5 were in most consensus. Our data strongly suggest that selection of particular sets of the 16S rRNA primers can impact microbiota analysis and interpretation of results in chicken as was shown previously for humans and other animal species.