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Douglas, Gavin M., Vincent J. Maffei, Jesse R. Zaneveld, Svetlana N. Yurgel, James R. Brown, Christopher M. Taylor, Curtis Huttenhower, and Morgan G. I. Langille. "PICRUSt2 for prediction of metagenome functions." Nature Biotechnology 38, no. 6 (June 2020): 685–88. http://dx.doi.org/10.1038/s41587-020-0548-6.
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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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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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Ha, Gwangsu, Hee-Jong Yang, Myeong-Seon Ryu, Su-Ji Jeong, Do-Youn Jeong, and Sunmin Park. "Bacterial Community and Anti-Cerebrovascular Disease-Related Bacillus Species Isolated from Traditionally Made Kochujang from Different Provinces of Korea." Microorganisms 9, no. 11 (October 27, 2021): 2238. http://dx.doi.org/10.3390/microorganisms9112238.
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Traditionally made Kochujang (TMK) is a long-term fermented soybean and rice mixture with red pepper and salts. The ambient bacteria in rice straw and nutrient components of Kochujang influence the bacteria community. We aimed to investigate the bacterial composition and quality of TMK from different provinces of Korea: Chungcheung (CC), Jeolla (JL), Kyungsang (KS), and GeongGee plus Kangwon (GK) provinces, and Jeju island (JJ). Furthermore, Bacillus spp. isolated from TMK were studied to have anti-cerebrovascular disease activity and probiotic properties. Seventy-three TMK samples from different regions were collected to assess the biogenic amine contents, bacteria composition using next-generation methods, and bacterial functions using Picrust2. Bacillus spp. was isolated from the collected TMK, and their antioxidant, fibrinolytic, and angiotensin I conversion enzyme (ACE) inhibitory activities and probiotic properties were examined. KS TMK had lower sodium contents than the other TMK. There were no significant differences in histamine and tyramine contents among the TMK samples in different provinces. The predominant bacteria in TMK was Bacillus spp., but KS included much less Bacillus spp. and higher Enterococcus and Staphylococcus than the other TMK. Gene expression related to lipopolysaccharide biosynthesis was higher in KS TMK than the other TMK in Picrust2. The predominant Bacillus spp. isolated from TMK was B. subtilis and B. velezensis. B. subtilis SRCM117233, SRCM117245, and SRCM117253 had antioxidant activity, whereas B. subtilis had higher fibrinolytic activity than other Bacillus spp. Only B. velezensis SRCM117254, SRCM117311, SRCM117314, and SRCM117318 had over 10% ACE inhibitory activity. In conclusion, KS had less Bacillus related to lower sodium contents than the other TMK. The specific strains of B. subtilis and B. velezensis had antioxidant, fibrinolytic, and ACE inhibitory activity, and they can be used as a starter culture to produce better quality controlled Kochujang with anti-cerebrovascular disease activities.
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Petry, Amy L., John F. Patience, Lucas R. Koester, Nichole F. Huntley, Michael R. Bedford, and Stephan Schmitz-Esser. "Xylanase modulates the microbiota of ileal mucosa and digesta of pigs fed corn-based arabinoxylans likely through both a stimbiotic and prebiotic mechanism." PLOS ONE 16, no. 1 (January 27, 2021): e0246144. http://dx.doi.org/10.1371/journal.pone.0246144.
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The experimental objective was to characterize the impact of insoluble corn-based fiber, xylanase, and an arabinoxylan-oligosaccharide on ileal digesta and mucosa microbiome of pigs. Three replicates of 20 gilts were blocked by initial body weight, individually-housed, and assigned to 1 of 4 dietary treatments: a low-fiber control (LF), a 30% corn bran high-fiber control (HF), HF+100 mg/kg xylanase (HF+XY), and HF+50 mg/kg arabinoxylan oligosaccharide (HF+AX). Gilts were fed their respective treatments for 46 days. On day 46, pigs were euthanized and ileal digesta and mucosa were collected. The V4 region of the 16S rRNA was amplified and sequenced, generating a total of 2,413,572 and 1,739,013 high-quality sequences from the digesta and mucosa, respectively. Sequences were classified into 1,538 mucosa and 2,495 digesta operational taxonomic units (OTU). Hidden-state predictions of 25 enzymes were made using Phylogenetic Investigation of Communities by Reconstruction of Unobserved States 2 (PICRUST2). Compared to LF, HF increased Erysipelotrichaceae_UCG-002, and Turicibacter in the digesta, Lachnospiraceae_unclassified in the mucosa, and decreased Actinobacillus in both (Q<0.05). Relative to HF, HF+XY increased 19 and 14 of the 100 most abundant OTUs characterized from digesta and mucosa, respectively (Q<0.05). Notably, HF+XY increased the OTU_23_Faecalibacterium by nearly 6 log2-fold change, compared to HF. Relative to HF, HF+XY increased genera Bifidobacterium, and Lactobacillus, and decreased Streptococcus and Turicibacter in digesta (Q<0.05), and increased Bifidobacterium and decreased Escherichia-Shigella in the mucosa (Q<0.05). Compared to HF, HF+AX increased 5 and 6 of the 100 most abundant OTUs characterized from digesta and mucosa, respectively, (Q<0.05), but HF+AX did not modulate similar taxa as HF+XY. The PICRUST2 predictions revealed HF+XY increased gene-predictions for enzymes associated with arabinoxylan degradation and xylose metabolism in the digesta, and increased enzymes related to short-chain fatty acid production in the mucosa. Collectively, these data suggest xylanase elicits a stimbiotic and prebiotic mechanism.
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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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Gu, Yaqiong, Beiying Li, Xiang Zhong, Conghe Liu, and Bin Ma. "Bacterial Community Composition and Function in a Tropical Municipal Wastewater Treatment Plant." Water 14, no. 10 (May 11, 2022): 1537. http://dx.doi.org/10.3390/w14101537.
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Bacterial diversity and community composition are of great importance in wastewater treatment; however, little is known about the diversity and community structure of bacteria in tropical municipal wastewater treatment plants (WWTPs). Therefore, in this study, activated sludge samples were collected from the return sludge, anaerobic sludge, anoxic sludge, and aerobic sludge of an A2O WWTP in Haikou, China. Illumina MiSeq high-throughput sequencing was used to examine the 16S ribosomal RNA (rRNA) of bacteria in the samples. The microbial community diversity in this tropical WWTP was higher than in temperate, subtropical, and plateau WWTPs. Proteobacteria, Bacteroidota, Patescibacteria, and Chloroflexi were the dominant phyla. Nitrification bacteria Nitrosomonas, and Nitrospira were also detected. Tetrasphaera, instead of Candidatus Accumulibacter, were the dominant polyphosphate accumulating organisms (PAOs), while, glycogen accumulating organisms (GAOs), such as Candidatus Competibacter and Defluviicoccus were also detected. The bacterial community functions predicted by PICRUSt2 were related to metabolism, genetic information processing, and environmental information processing. This study provides a reference for the optimization of tropical municipal WWTPs.
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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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Santibáñez, Rodrigo, Felipe Lara, Teresa M. Barros, Elizabeth Mardones, Françoise Cuadra, and Pamela Thomson. "Ocular Microbiome in a Group of Clinically Healthy Horses." Animals 12, no. 8 (April 7, 2022): 943. http://dx.doi.org/10.3390/ani12080943.
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The ocular microbiome in horses is poorly described compared to other species, and most of the information available in the literature is based on traditional techniques, which has limited the depth of the knowledge on the subject. The objective of this study was to characterize and predict the metabolic pathways of the ocular microbiome of a group of healthy horses. Conjunctival swabs were obtained from both eyes of 14 horses, and DNA extraction was performed from the swabs, followed by next generation sequencing and bioinformatics analyses employing DADA2 and PICRUSt2. A total of 17 phyla were identified, of which Pseudomonadota (Proteobacteria) was the most abundant (59.88%), followed by Actinomycetota (Actinobacteria) (22.44%) and Bacteroidota (Bacteroidetes) (16.39%), totaling an average of 98.72% of the communities. Similarly, of the 278 genera identified, Massilia, Pedobacter, Pseudomonas, Sphingomonas, Suttonella and Verticia were present in more than 5% of the samples analyzed. Both Actinobacteria and Bacteroides showed great heterogeneity within the samples. The most abundant inferred metabolic functions were related to vital functions for bacteria such as aerobic respiration, amino acid, and lipid biosynthesis.
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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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Wu, Haoming, Yang Wang, Lei Dong, Haiyan Hu, Lu Meng, Huimin Liu, Nan Zheng, and Jiaqi Wang. "Microbial Characteristics and Safety of Dairy Manure ComPosting for Reuse as Dairy Bedding." Biology 10, no. 1 (December 28, 2020): 13. http://dx.doi.org/10.3390/biology10010013.
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Changes in bacterial community, phenotype, metabolic function, and pathogenic bacteria content in recycled manure solids (RMS) were analyzed by 16S rRNA sequencing, Bugbase, picrost2, and qPCR, respectively. The data from RMS bedding were compared to those of sand bedding and rice husk bedding. The results show that the proportion of potentially pathogenic bacteria among the manure flora of RMS after dry and wet separation, after composting, and after sun-cure storage was 74.00%, 26.03%, and 49.067%, respectively. Compared to RMS bedding, the proportion of potentially pathogenic microorganisms in sand bedding and rice husk bedding was higher. The picrust2 analyses show that the level of lipopolysaccharide biosynthesis changed significantly during RMS processing. In addition, the qPCR results show that composting could effectively reduce the detection and quantification of pathogens, except Streptococcus uberis, in RMS bedding. In general, composting is an essential step to improve the safety of bedding materials in the process of fecal treatment. However, at the same time, RMS bedding may increase the risk of mastitis caused by Streptococcus uberis.
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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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Yildirim, Elena, Larisa Ilina, Georgy Laptev, Valentina Filippova, Evgeni Brazhnik, Timur Dunyashev, Andrey Dubrovin, et al. "The structure and functional profile of ruminal microbiota in young and adult reindeers (Rangifer tarandus) consuming natural winter-spring and summer-autumn seasonal diets." PeerJ 9 (November 24, 2021): e12389. http://dx.doi.org/10.7717/peerj.12389.
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Background The key natural area of Russian reindeer (Rangifer tarandus, Nenets breed) is arctic zones, with severe climatic conditions and scarce feed resources, especially in the cold winter season. The adaptation of reindeer to these conditions is associated not only with the genetic potential of the animal itself. The rumen microbiome provides significant assistance in adapting animals to difficult conditions by participating in the fiber digestion. The aim of our study is to investigate the taxonomy and predicted metabolic pathways of the ruminal microbiota (RM) during the winter–spring (WS) and summer–autumn (SA) seasons, in calves and adult reindeer inhabiting the natural pastures of the Yamalo-Nenetsky Autonomous District of the Russian Federation. Methods The RM in reindeer was studied using the Next Generation Sequencing method with the MiSeq (Illumina, San Diego, CA, USA) platform. Reconstruction and prediction of functional profiles of the metagenome, gene families, and enzymes were performed using the software package PICRUSt2 (v.2.3.0). Results The nutritional value of WS and SA diets significantly differed. Crude fiber content in the WS diet was higher by 22.4% (p < 0.05), compared to SA, indicating possibly poorer digestibility and necessity of the adaptation of the RM to this seasonal change. A total of 22 bacterial superphyla and phyla were found in the rumen, superphylum Bacteroidota and phylum Firmicutes being the dominating taxa (up to 48.1% ± 4.30% and 46.1% ± 4.80%, respectively); while only two archaeal phyla presented as minor communities (no more then 0.54% ± 0.14% totally). The percentages of the dominating taxa were not affected by age or season. However, significant changes in certain minor communities were found, with seasonal changes being more significant than age-related ones. The percentage of phylum Actinobacteriota significantly increased (19.3-fold) in SA, compared to WS (p = 0.02) in adults, and the percentage of phylum Cyanobacteria increased up to seven-fold (p = 0.002) in adults and calves. Seasonal changes in RM can improve the ability of reindeer to withstand the seasons characterized by a low availability of nutrients. The PICRUSt2 results revealed 257 predicted metabolic pathways in RM: 41 pathways were significantly (p < 0.05) influenced by season and/or age, including the processes of synthesis of vitamins, volatile fatty acids, and pigments; metabolism of protein, lipids, and energy; pathogenesis, methanogenesis, butanediol to pyruvate biosynthesis, cell wall biosynthesis, degradation of neurotransmitters, lactic acid fermentation, and biosynthesis of nucleic acids. A large part of these changeable pathways (13 of 41) was related to the synthesis of vitamin K homologues. Conclusion The results obtained improve our knowledge on the structure and possible metabolic pathways of the RM in reindeer, in relation to seasonal changes.
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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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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, 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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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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Nakayasu, Masaru, Kyoko Ikeda, Shinichi Yamazaki, Yuichi Aoki, Kazufumi Yazaki, Haruhiko Washida, and Akifumi Sugiyama. "Two Distinct Soil Disinfestations Differently Modify the Bacterial Communities in a Tomato Field." Agronomy 11, no. 7 (July 7, 2021): 1375. http://dx.doi.org/10.3390/agronomy11071375.
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Reductive soil disinfestation (RSD) and soil solarization (SS) were evaluated based on environmental factors, microbiome, and suppression of Fusarium oxysporum in a tomato field soil. Soil environmental factors (moisture content, electric conductivity, pH, and redox potential (RP)) were measured during soil disinfestations. All factors were more strongly influenced by RSD than SS. 16S rRNA amplicon sequencing of RSD- and SS-treated soils was performed. The bacterial communities were taxonomically and functionally distinct depending on treatment methods and periods and significantly correlated with pH and RP. Fifty-four pathways predicted by PICRUSt2 (third level in MetaCyc hierarchy) were significantly different between RSD and SS. Quantitative polymerase chain reaction demonstrated that both treatments equally suppressed F. oxysporum. The growth and yield of tomato cultivated after treatments were similar between RSD and SS. RSD and SS shaped different soil bacterial communities, although the effects on pathogen suppression and tomato plant growth were comparable between treatments. The existence of pathogen-suppressive microbes, other than Clostridia previously reported to have an effect, was suggested. Comparison between RSD and SS provides new aspects of unknown disinfestation patterns and the usefulness of SS as an alternative to RSD.
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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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Morales-Rivera, María F., Diego Valenzuela-Miranda, Gustavo Nuñez-Acuña, Bárbara P. Benavente, Cristian Gallardo-Escárate, and Valentina Valenzuela-Muñoz. "Atlantic Salmon (Salmo salar) Transfer to Seawater by Gradual Salinity Changes Exhibited an Increase in The Intestinal Microbial Abundance and Richness." Microorganisms 11, no. 1 (December 27, 2022): 76. http://dx.doi.org/10.3390/microorganisms11010076.
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The host’s physiological history and environment determine the microbiome structure. In that sense, the strategy used for the salmon transfer to seawater after parr-smolt transformation may influence the Atlantic salmon’s intestinal microbiota. Therefore, this study aimed to explore the diversity and abundance of the Atlantic salmon intestinal microbiota and metagenome functional prediction during seawater transfer under three treatments. One group was exposed to gradual salinity change (GSC), the other to salinity shock (SS), and the third was fed with a functional diet (FD) before the seawater (SW) transfer. The microbial profile was assessed through full-16S rRNA gene sequencing using the Nanopore platform. In addition, metagenome functional prediction was performed using PICRUSt2. The results showed an influence of salinity changes on Atlantic salmon gut microbiota richness, diversity, and taxonomic composition. The findings reveal that GSC and the FD increased the Atlantic salmon smolt microbiota diversity, suggesting a positive association between the intestinal microbial community and fish health during seawater transfer. The reported knowledge can be applied to surveil the microbiome in smolt fish production, improving the performance of Atlantic salmon to seawater transfer.
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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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Silva, Marliane de Cássia Soares, Tomás Gomes Reis Veloso, Thaynara Lorenzoni Entringer, Vilian Borchardt Bullergahn Borchardt Bullergahn, Lucas Louzada Pereira, Larissa Márcia Anastácio, and Maria Catarina Megumi Kasuya. "DIVERSITY OF NITROGEN-FIXING BACTERIA IN COFFEE CROPS (Coffea arabica L.)." Revista Ifes Ciência 6, no. 3 (December 23, 2020): 12–21. http://dx.doi.org/10.36524/ric.v6i3.852.
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Abstract: Microorganisms play a crucial role in plant growth and development. Nitrogen-Fixing Bacteria (NFB), for instance, are essential to nitrogen nutrition. However, few studies have focused on this important community of coffee agrosystems. Therefore, this study aims to evaluate the diversity of NFB in soil and fruits from eight coffee farms. After DNA extraction, the V4 hypervariable region of 16S rDNA was amplified and sequenced in Illumina MiSeq sequencer. The prediction of potential nitrogen-fixing bacteria was performed by PICRUSt2. One hundred and eighteen ASVs were predicted as potential nitrogen-fixing. While 115 ASVs were detected in fruits, only four were found in fruits. The most abundant phylum was Proteobacteria (71 %), followed by Firmicutes (23 %). The relative abundance of the NFB concerning the whole bacterial community ranged from three to almost six percent. Only one ASV of the Rhizobiaceae family was found, simultaneously, in fruits and soil. The Bradyrhizobium genus was found in all soil samples. We conclude that important NFB are part of the microbiota present in the soil and coffee fruit and that there is a sharing between them. There is evidences that Bradyrhizobium genus can be considered a significant component of the core microbiota in coffee soil.
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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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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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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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Coelho, Catarina, Igor Tiago, and António Veríssimo. "Guts Bacterial Communities of Porcellio dilatatus: Symbionts Predominance, Functional Significance and Putative Biotechnological Potential." Microorganisms 10, no. 11 (November 11, 2022): 2230. http://dx.doi.org/10.3390/microorganisms10112230.
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Terrestrial isopods are effective herbivorous scavengers with an important ecological role in organic matter cycling. Their guts are considered to be a natural enrichment environment for lignocellulosic biomass (LCB)-degrading bacteria. The main goal of this work was to assess the structural diversity of Porcellio dilatatus gut bacterial communities using NGS technologies, and to predict their functional potential using PICRUSt2 software. Pseudomonadota, Actinomycetota, Bacillota, Cyanobacteria, Mycoplasmatota, Bacteroidota, Candidatus Patescibacteria and Chloroflexota were the most abundant phyla found in P. dilatatus gut bacterial communities. At a family level, we identified the presence of eleven common bacterial families. Functionally, the P. dilatatus gut bacterial communities exhibited enrichment in KEGG pathways related to the functional module of metabolism. With the predicted functional profile of P. dilatatus metagenomes, it was possible to envision putative symbiotic relationships between P. dilatatus gut bacterial communities and their hosts. It was also possible to foresee the presence of a well-adapted bacterial community responsible for nutrient uptake for the host and for maintaining host homeostasis. Genes encoding LCB-degrading enzymes were also predicted in all samples. Therefore, the P. dilatatus digestive tract may be considered a potential source of LCB-degrading enzymes that is not to be neglected.
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Tang, Qiuxiang, Xiaoru Chen, Jun Huang, Suyi Zhang, Hui Qin, Yi Dong, Chao Wang, et al. "Mechanism of Enhancing Pyrazines in Daqu via Inoculating Bacillus licheniformis with Strains Specificity." Foods 12, no. 2 (January 9, 2023): 304. http://dx.doi.org/10.3390/foods12020304.
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Despite the importance of pyrazines in Baijiu flavor, inoculating functional strains to increase the contents of pyrazine in Daqu and how those interact with endogenic communities is not well characterized. The effects of inoculating Bacillus licheniformis with similar metabolic capacity on pyrazine and community structure were assessed in the Daqu complex system and compared with traditional Daqu. The fortification strategy increased the volatile metabolite content of Daqu by 52.40% and the pyrazine content by 655.99%. Meanwhile, results revealed that the pyrazine content in Daqu inoculated isolate J-49 was 2.35–7.41 times higher than isolate J-41. Both isolates have the almost same capability of 2,3-butanediol, a key precursor of pyrazine, in pure cultured systems. Since the membrane fatty acids of isolate J-49 contain unsaturated fatty acids, it enhances the response-ability to withstand complex environmental pressure, resulting in higher pyrazine content. PICRUSt2 suggested that the increase in pyrazine was related to the enzyme expression of nitrogen metabolism significantly increasing, which led to the enrichment of NH4+ and 2,3-butanediol (which increased by 615.89%). These results based on multi-dimensional approaches revealed the effect of functional bacteria enhancement on the attribution of Daqu, laid a methodological foundation regulating the microbial community structure and enhanced the target products by functional strains.
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Si, Yan-Ji, Yang Xu, Bin-Qi Li, Jin Liu, Li-Peng Meng, Yu Li, Rui-Qing Ji, and Shu-Yan Liu. "Ectomycorrhizospheric Microbiome Assembly Rules of Quercus mongolica in the Habitat of SongRong (Tricholoma matsutake) and the Effect of Neighboring Plants." Diversity 14, no. 10 (September 28, 2022): 810. http://dx.doi.org/10.3390/d14100810.
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Host plants are known to determine the distribution and development of ectomycorrhizal fungi such as Tricholoma matsutake; however, we found that the fruit body distribution of T. matsutake was different in Quercus mongolica pure or mixed forests. To clarify the fungal and other microbial composition rules of host plants, ectomycorrhizal root tip samples of Q. mongolica mixed with different plants were selected for study. By using high-throughput sequencing, we obtained 5229 fungal and 38,834 bacterial amplicon sequence variants (ASVs) as determined by internally transcribed spacer ribosomal RNA (ITS rRNA) and 16S ribosomal RNA (16S rRNA) sequencing via the Illumina NovaSeq platform. Among the neighboring plants, there were no significant differences in fungal or bacterial alpha diversity, but there was a significant difference (p < 0.05) in ectomycorrhizal alpha diversity. The fungal, bacterial and ectomycorrhizal fungal communities in the ectomycorrhizosphere of Q. mongolica all showed differences in beta diversity and species composition. In addition, the physical and chemical properties of the soil and the relationships among species could affect the relative abundance of fungi, bacteria and ectomycorrhizal fungi, but the soil microbial pool had little effect on microbial composition. Using PICRUSt2, some significantly up-regulated (p < 0.05) metabolic functions in ectomycorrrhizospheric microbial communities were predicted, which would be an interesting research field for ectomycorrhizal microecology.
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Baquiran, Jake Ivan P., Michael Angelou L. Nada, Niño Posadas, Dana P. Manogan, Patrick C. Cabaitan, and Cecilia Conaco. "Population structure and microbial community diversity of two common tetillid sponges in a tropical reef lagoon." PeerJ 8 (April 22, 2020): e9017. http://dx.doi.org/10.7717/peerj.9017.
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Sponges are predicted to dominate future reef ecosystems influenced by anthropogenic stressors and global climate change. The ecological success of sponges is attributed to their complex physiology, which is in part due to the diversity of their associated prokaryotic microbiome. However, the lack of information on the microbial community of many sponge species makes it difficult to gauge their interactions and functional contributions to the ecosystem. Here, we investigated the population dynamics and microbial community composition of two tetillid sponges identified as Cinachyrella sp. and Paratetilla sp., which are common on coral bommies in a reef lagoon in Bolinao, northwestern Philippines. The sponges ranged in size from 2.75 ± 2.11 to 6.33 ± 3.98 cm (mean ± standard deviation) and were found at an average density of 1.57 ± 0.79 to 4.46 ± 3.60 individuals per sq. m. on the bommies. The tetillid sponge population structure remained stable over the course of four years of monitoring. Prokaryotic communities associated with the sponges were distinct but had overlapping functions based on PICRUSt2 predictions. This convergence of functions may reflect enrichment of metabolic processes that are crucial for the survival of the tetillid sponges under prevailing conditions in the reef lagoon. Differentially enriched functions related to carbon, sulfur, fatty acid, and amino acid metabolism, cellular defense, and stress response, may influence the interactions of tetillid sponges with other biota on the bommies.
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Ortíz-López, Guadalupe, and Luz Breton Deval. "Ecología microbiana de minas de cobre de seis diferentes regiones geográficas." Revista Internacional de Contaminación Ambiental 38, Ambiente y Bioenergía (September 2, 2022): 143–54. http://dx.doi.org/10.20937/rica.54294.
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El objetivo del trabajo fue comparar la estructura de las comunidades microbianas de minas de cobre de diferentes regiones geográficas con la finalidad de encontrar patrones en la composición de las comunidades y dilucidar su potencial metabólico. Los amplicones de las minas localizadas en Brasil, Canadá, China, Portugal, Reino Unido y Bulgaria se obtuvieron del Sequence Read Archive (SRA) del sitio web del National Center for Biotechnology Information (NCBI). El estudio bioinformático para la repartición taxonómica se realizó con la plataforma Qiime2. Se determinaron la abundancia relativa, la diversidad y su correlación con parámetros físicos y químicos usando R Studio. Posteriormente, se realizó la predicción funcional con PICRUSt2. Los resultados muestran que la mina de Reino Unido es donde se presenta el mayor número de clases y la mina de Bulgaria es la menos diversa. Gammaproteobacteria, Actinobacteria y Alphaproteobacteria son las clases más abundantes en todas las minas y cuentan con géneros que poseen características metabólicas relacionadas con la oxidación o reducción de metales. Las predicciones funcionales sugieren la presencia de genes relacionados con la reducción de metales pesados como cobre y mercurio. Las minas de cobre de diferentes regiones presentan un patrón similar de clases encontradas a pesar de que existen diferencias puntuales de clases bacterianas que atribuimos a la presión de las condiciones físicas y químicas.
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Ibal, Jerald-Conrad, Min-Kyu Park, Gun-Seok Park, Byung-Kwon Jung, Tae-Hyung Park, Min-Sueng Kim, Gi-Ung Kang, Yeong-Jun Park, and Jae-Ho Shin. "Use of Acyl-Homoserine Lactones Leads to Improved Growth of Ginseng Seedlings and Shifts in Soil Microbiome Structure." Agronomy 11, no. 11 (October 28, 2021): 2177. http://dx.doi.org/10.3390/agronomy11112177.
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Panax ginseng is a well-known medicinal plant that achieves strong resistance against plant pathogens while growing in the wild. Due to the high market demand for ginseng as a health food source, ginseng cultivation is prevalent in South Korea. However, continuous monocropping creates problems like irregular growth or vulnerability to crop diseases. Quorum sensing (QS) deals with the intracellular communication of bacteria and plays a role in dynamic changes in the soil microbiome. Here, we investigated how acyl-homoserine lactone (AHL) signaling molecules in QS (C8, C10, and C12) improve plant growth and induce shifts in the soil microbiome. To assess the effects, we recorded root and shoot growth of ginseng seedlings and checked the changes in the soil microbiome during different time points (0, 2, 4, and 8) after 8 weeks of growth. We observed that soils treated with N-decanoyl-L-homoserine lactone (C10) showed the most pronounced effects. Very striking was that C10 had the lowest alpha diversity. Using Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt2), we observed a high number of QS-related functional genes, with the highest count occurring in the untreated planted soil (W). Together with the known direct and beneficial effects of AHLs on plant development, AHLs treated mono-cropped soil showed trends in the microbiome community.
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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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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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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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Shahinozzaman, Md, Samnhita Raychaudhuri, Si Fan, and Diana N. Obanda. "Kale Attenuates Inflammation and Modulates Gut Microbial Composition and Function in C57BL/6J Mice with Diet-Induced Obesity." Microorganisms 9, no. 2 (January 24, 2021): 238. http://dx.doi.org/10.3390/microorganisms9020238.
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Kale (Brassica oleracea var. acephala) is a vegetable common in most cultures but is less studied as a functional food compared to other cruciferous vegetables, such as broccoli. We investigated the effect of supplementing a high-fat diet (HFD) with kale (HFKV) in C57BL/6J mice. We particularly explored its role in metabolic parameters, gut bacterial composition and diversity using 16S rRNA sequencing, systematically compared changes under each phylum and predicted the functional potential of the altered bacterial community using PICRUSt2. Like other cruciferous vegetables, kale attenuated HFD-induced inflammation. In addition, kale modulated HFD-induced changes in cecal microbiota composition. The HFD lowered bacterial diversity, increased the Firmicutes: Bacteroidetes (F/B) ratio and altered composition. Specifically, it lowered Actinobacteria and Bacteroidetes (Bacteroidia, Rikenellaceae and Prevotellaceae) but increased Firmicutes (mainly class Bacilli). Kale supplementation lowered the F/B ratio, increased both alpha and beta diversity and reduced class Bacilli and Erysipelotrichi but had no effect on Clostridia. Within Actinobacteria, HFKV particularly increased Coriobacteriales/Coriobacteriaceae about four-fold compared to the HFD (p < 0.05). Among Bacteroidia, HFKV increased the species Bacteroides thetaiotaomicron by over two-fold (p = 0.05) compared to the HFD. This species produces plant polysaccharide digesting enzymes. Compared to the HFD, kale supplementation enhanced several bacterial metabolic functions, including glycan degradation, thiamine metabolism and xenobiotic metabolism. Our findings provide evidence that kale is a functional food that modulates the microbiota and changes in inflammation phenotype.
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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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Das, Bikram K., Satoshi Ishii, Linto Antony, Alexander J. Smart, Joy Scaria, and Volker S. Brözel. "The Microbial Nitrogen Cycling, Bacterial Community Composition, and Functional Potential in a Natural Grassland Are Stable from Breaking Dormancy to Being Dormant Again." Microorganisms 10, no. 5 (April 28, 2022): 923. http://dx.doi.org/10.3390/microorganisms10050923.
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The quantity of grass-root exudates varies by season, suggesting temporal shifts in soil microbial community composition and activity across a growing season. We hypothesized that bacterial community and nitrogen cycle-associated prokaryotic gene expressions shift across three phases of the growing season. To test this hypothesis, we quantified gene and transcript copy number of nitrogen fixation (nifH), ammonia oxidation (amoA, hao, nxrB), denitrification (narG, napA, nirK, nirS, norB, nosZ), dissimilatory nitrate reduction to ammonia (nrfA), and anaerobic ammonium oxidation (hzs, hdh) using the pre-optimized Nitrogen Cycle Evaluation (NiCE) chip. Bacterial community composition was characterized using V3-V4 of the 16S rRNA gene, and PICRUSt2 was used to draw out functional inferences. Surprisingly, the nitrogen cycle genes and transcript quantities were largely stable and unresponsive to seasonal changes. We found that genes and transcripts related to ammonia oxidation and denitrification were different for only one or two time points across the seasons (p < 0.05). However, overall, the nitrogen cycling genes did not show drastic variations. Similarly, the bacterial community also did not vary across the seasons. In contrast, the predicted functional potential was slightly low for May and remained constant for other months. Moreover, soil chemical properties showed a seasonal pattern only for nitrate and ammonium concentrations, while ammonia oxidation and denitrification transcripts were strongly correlated with each other. Hence, the results refuted our assumptions, showing stability in N cycling and bacterial community across growing seasons in a natural grassland.
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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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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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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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Das, Bikram K., Robiul Islam Rubel, Surbhi Gupta, Yajun Wu, Lin Wei, and Volker S. Brözel. "Impacts of Biochar-Based Controlled-Release Nitrogen Fertilizers on Soil Prokaryotic and Fungal Communities." Agriculture 12, no. 10 (October 16, 2022): 1706. http://dx.doi.org/10.3390/agriculture12101706.
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Controlled-release Nitrogen Fertilizers (CRNFs) are an effective fertilization technique by minimizing nutrient loss and making Nitrogen (N) available to plants as they grow. Biochar-based CRNF (BCRNF) technologies have been demonstrated very promising in increase of corn yield. Despite the beneficial effects of BCRNFs, their impacts on prokaryotic and fungal soil communities are not well evaluated. Different formulations of BCRNF were developed to investigate their effects on corn productivity. We analyzed the soil microbes and their functional potential under different BCRNF regimes using amplified V3–V4 region of 16s rRNA for determining prokaryotic, and ITS genes for fungal communities. The soil prokaryotic diversity was similar across the treatments, with differences in prokaryotic genera with relative abundance of 0.1% or less in the soil (p < 0.05). In contrast, the fungal community diversity was different only for unfertilized soil. It had a high relative abundance for Aspergillus. Genus level comparison showed that Pseudofabraea was higher in Bioasphalt-based BCRNF compared to other treatments. Moreover, the N-fixing communities in soil were also similar across the treatments. At genus level, Microvirga, Azospirillum, and Methyloprofundus were highest in no-fertilizer control. The functional potential predictions using PICRUSt2 portrayed a consistent N-cycling functions across the treatments. However, the predicted gene functions related to nitrous-oxide reductase (nosZ) and hydroxylamine reductase (hcp) were significantly lower in soil receiving BCRNF containing biosolid. Overall, BCRNF treatments previously identified to increase corn yield displayed minimal shifts in the soil microbial communities. Thus, such novel fertilization would enable increased crop yield without affecting soil communities leading to sustainable crop production.
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Zhuang, Yuqi, Yadong Xu, Meiling Yang, Huiru Zhao, and Xinping Ye. "Impacts of Japanese Larch Invasion on Soil Bacterial Communities of the Giant Panda Habitat in the Qinling Mountains." Microorganisms 10, no. 9 (September 9, 2022): 1807. http://dx.doi.org/10.3390/microorganisms10091807.
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Japanese larch (Larix kaempferi), a non-native tree species, has been widely planted in the Qinling Mountains since the last century, but it does not meet the habitat needs of giant pandas (Ailuropoda melanoleuca), mainly because of food, further causing habitat degradation and fragmentation. However, how soil microorganisms, considered as predictors of the soil environment, respond to Japanese larch remains poorly explored, especially compared with native forests. Here, we collected 40 soil samples from plantation, bamboo, and natural (excluding bamboo) forests in the Changqing Nature Reserve and Foping Nature Reserve in Qinling to compare soil bacterial community composition and diversity using high-throughput sequencing of bacterial 16S rRNA genes. The soil chemical properties and bacterial communities differed noticeably under forest-type classification patterns. The soil of the Japanese larch planted forests underwent substantial degradation, with higher acidity, lower alpha diversity, and more significant enrichment in the oligotrophic bacteria Acidobacteria and Verrucomicrobia, in contrast to the other two primary forests with elevated soil nutrient levels. The application of PICRUSt2 indicated the down-regulation of amino acid-related metabolism in planted forests. Moreover, pH was the primary factor determining the whole bacterial community structures. To avoid the uncertainty of a single sampling region, we chose different sampling sites that could be considered as geographical factors, possibly due to environmental heterogeneity or dispersal limitations, which also explained the specific community patterns of microorganisms. Overall, this paper may help provide a scientific basis for future revegetation in giant panda habitats, highlighting the urgent need for ecological restoration and sustainable forestry management.
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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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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.