Academic literature on the topic 'PICRUSt2 analysis'
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Journal articles on the topic "PICRUSt2 analysis"
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Zhao, Qiong, Fengxing Xie, Fengfeng Zhang, Ke Zhou, Haibo Sun, Yujie Zhao, and Qian Yang. "Analysis of bacterial community functional diversity in late-stage shrimp (Litopenaeus vannamei) ponds using Biolog EcoPlates and PICRUSt2." Aquaculture 546 (January 2022): 737288. http://dx.doi.org/10.1016/j.aquaculture.2021.737288.
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Baltazar-Díaz, Tonatiuh Abimael, Luz Alicia González-Hernández, Juan Manuel Aldana-Ledesma, Marcela Peña-Rodríguez, Alejandra Natali Vega-Magaña, Adelaida Sara Minia Zepeda-Morales, Rocío Ivette López-Roa, et al. "Escherichia/Shigella, SCFAs, and Metabolic Pathways—The Triad That Orchestrates Intestinal Dysbiosis in Patients with Decompensated Alcoholic Cirrhosis from Western Mexico." Microorganisms 10, no. 6 (June 16, 2022): 1231. http://dx.doi.org/10.3390/microorganisms10061231.
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Gut microbiota undergoes profound alterations in alcohol cirrhosis. Microbiota-derived products, e.g., short chain fatty acids (SCFA), regulate the homeostasis of the gut-liver axis. The objective was to evaluate the composition and functions of the intestinal microbiota in patients with alcohol-decompensated cirrhosis. Fecal samples of 18 patients and 18 healthy controls (HC) were obtained. Microbial composition was characterized by 16S rRNA amplicon sequencing, SCFA quantification was performed by gas chromatography (GC), and metagenomic predictive profiles were analyzed by PICRUSt2. Gut microbiota in the cirrhosis group revealed a significant increase in the pathogenic/pathobionts genera Escherichia/Shigella and Prevotella, a decrease in beneficial bacteria, such as Blautia, Faecalibacterium, and a decreased α-diversity (p < 0.001) compared to HC. Fecal SCFA concentrations were significantly reduced in the cirrhosis group (p < 0.001). PICRUSt2 analysis indicated a decrease in acetyl-CoA fermentation to butyrate, as well as an increase in pathways related to antibiotics resistance, and aromatic amino acid biosynthesis. These metabolic pathways have been poorly described in the progression of alcohol-related decompensated cirrhosis. The gut microbiota of these patients possesses a pathogenic/inflammatory environment; therefore, future strategies to balance intestinal dysbiosis should be implemented. These findings are described for the first time in the population of western Mexico.
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Ponomareva, E. S., E. A. Yildirim, V. A. Filippova, L. A. Ilina, A. V. Dubrowin, G. Y. Laptev, K. A. Kalitkina, T. P. Dunyashev, and D. G. Tiurina. "Comparison of the composition and metabolic potential of the reindeer’s rumen microbiome in the Yamal-Nenets and Nenets autonomous district of the Russian Arctic." Acta Biomedica Scientifica 7, no. 3 (July 5, 2022): 30–37. http://dx.doi.org/10.29413/abs.2022-7.3.4.
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The adaptive ability of reindeer to the harsh conditions of the Russian Arctic is not determined solely by the genome of the macroorganism and, of course, includes an extensive genetic and metabolic repertoire of the microbiome.The aim. To compare the taxonomic and predicted metabolic profiles of the rumen microbiome of adult reindeer living in the natural pastures of the Yamalo-Nenets and Nenets Autonomous districts of the Russian Federation.Materials and methods. Expeditions to the Yamal-Nenets and Nenets Autonomous districts of the Russian Arctic in 2017 were carried out to take samples of the rumen. The contents of the rumen were taken from clinically healthy reindeer individuals (at least 3 times repetition). To analyze the animal scar microbiota and determine metabolic profiles, 16S rRNA NGS sequencing was performed on a MiSeq device (Illumina, USA). Bioinformatic data analysis was performed using QIIME2 software ver. 2020.8. The noise sequences were filtered by DADA2. Silva 138 reference database was used for taxonomy analysis. Reconstruction and prediction of the functional content of the metagenome was carried out using the software complex PICRUSt2 (v. 2.3.0).Results. During NGS sequencing, a total of 223 768 sequences of the 16S rRNA gene of the reindeer scarring microbiome were studied. Significant (p ≤ 0.05) differences between the groups in 10 bacterial phyla and superphyla were revealed: Actinobacteriota, Spirochaetes, Chloroflexi, Verrucomicrobia, Bdellovibrionota, Synergistetes, Fusobacteriota, Myxococcota, Cyanobacteria, Campilobacterota. The results of the reconstruction and prediction of the functional content of the metagenome using the PICRUSt2 bioinformatic analysis made it possible to identify 328 potential metabolic pathways. Differences between the groups were revealed in 16 predicted metabolic pathways, among which the pathways of chlorophyllide and amino acid biosynthesis dominated.
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Jeong, Su-Ji, Myeong-Seon Ryu, Hee-Jong Yang, Xuan-Hao Wu, Do-Youn Jeong, and Sun-Min Park. "Bacterial Distribution, Biogenic Amine Contents, and Functionalities of Traditionally Made Doenjang, a Long-Term Fermented Soybean Food, from Different Areas of Korea." Microorganisms 9, no. 7 (June 22, 2021): 1348. http://dx.doi.org/10.3390/microorganisms9071348.
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Since doenjang quality depends on the bacterial composition, which ambient bacteria in the environment and production conditions influence, a complete understanding of the bacteria community in traditionally madetraditionally made doenjang (TMD) from different regions is needed. We aimed to investigate the bacteria composition and quality of TMD in the following areas: Chonbuk (CB), Chonnam (CN), Kyungsang (KS), Kangwon (KW), Chungchung (CC) provinces, and Jeju island (JJ) of Korea. Twenty-nine TMD samples from different regions were used to assess biogenic amine contents, bacteria composition using next-generation methods, and metabolic functions of the bacteria using Picrust2. Bacillus spp. were isolated, and their antioxidant and fibrinolytic activities were determined. Most TMD contained high amounts of beneficial bacteria (Bacillus, Lactobacillus, Pediococcus and Weissella). However, some KS samples contained harmful bacteria (Cronobacter, Proteus and Acinetobacter) and less beneficial B. velezensis bacteria. There was no similarity among the regional groups, and each TMD showed a different bacteria composition. Shannon index, α-diversity index, was lower in TMD from JJ and CB than the other areas, but there was no β-diversity among TMD from the six area groups. Picrust2 analysis revealed that the functional potential for arachidonic acid metabolism was lowest in JJ and CN, that for supporting insulin action was highest in KS and JJ, and that for carbohydrate digestion and absorption was lowest in CB and JJ among all groups (p < 0.05) according to the Kyoto Encyclopedia of Genes and Genomes Orthology. Histamine contents were lower in CN and CC, and tyramine contents did not differ significantly. B. velezensis, B. subtilis, B. licheniformis, B. siamensis, and B. amyloliquefaciens were isolated from TMD. None of the isolated Bacillus spp. contained the B. cereus gene. B. subtilis from CN had the highest fibrinolytic activity, and B. velezensis from CB had the highest antioxidant activity. In conclusion, TMD mainly contained various Bacillus spp., and the predominant one was B. velezensis, which had antioxidant and fibrinolytic activity regardless of the regional origin.
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Guo, Manli, Zhidong Zhang, Jiyuan Lu, Di Wang, Yimin Yan, Shen Zhang, Xin Yu, et al. "Differences in Supragingival Microbiome in Patients with and without Full-Crown Prostheses." Dentistry Journal 10, no. 8 (August 15, 2022): 152. http://dx.doi.org/10.3390/dj10080152.
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Objectives: To characterize the microflora profile of supragingival biofilm in patients with and without full-crown prostheses. Methods: Plaque samples of full-crown prostheses and teeth in patients with porcelain-fused-to-metal crowns, all-ceramic crowns, and no prostheses were collected (three patients per group), using 16S rRNA high-throughput sequencing technology to conduct DNA sequencing on the samples and using Qiime, R, and PICRUSt2 software to perform bioinformatics analyses and functional analyses on sequencing data. Results: In total, 110,209 valid sequences were obtained in the experiment, corresponding to 11 phyla and 120 genera. The predominant species shared by the three groups were phyla Actinobacteria, Bacteroidetes, Firmicutes, Fusobacteria, and Proteobacteria and genera Rothia, Porphyromonas, Prevotella, Streptococcus, Veillonella, Leptotrichia, Neisseria, Citrobacter, and Pseudomonas. The species-difference analysis showed that genus Hameophilus significantly increased after the patient wore the dental prosthesis. Compared with the no-prosthesis samples, the functional analysis showed that cell motility increased in the samples from full-crown prostheses, while replication and repair, and translation decreased. Conclusions: This study reveals the changes in the oral microbial community of patients with full-crown prostheses, which could provide insights regarding the safety of materials for long-term use in the oral cavity.
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Bierwirth, S., A. Sorbie, O. Coleman, E. Reuß, P. Weber, N. Köhler, T. Kacprowski, et al. "P057 Mucosal microbiota adapts to ATF6-induced alterations in host lipid metabolism with prognostic value in colorectal cancer." Journal of Crohn's and Colitis 16, Supplement_1 (January 1, 2022): i167. http://dx.doi.org/10.1093/ecco-jcc/jjab232.186.
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Abstract Background Colorectal cancer (CRC) is a leading cause of cancer deaths worldwide. The endoplasmic reticulum unfolded protein response (UPRER) signal transducer activating transcription factor 6 (ATF6) is a clinically relevant pre-cancerous marker in CRC and colitis-associated CRC. We established the interrelated role of the microbiota and ATF6 signalling as a novel tumor-promoting mechanism in our transgenic mouse model of spontaneous microbiota-dependent ATF6-driven CRC (nATF6IEC). Methods To elucidate the transcriptional program initiated by acute and chronic ATF6 signalling, mRNA sequencing analyses of murine colonic intestinal epithelial cells were performed 4 days or 5 weeks after induction of ATF6, respectively. Germfree (GF) mice served to dissect microbiota contribution to the transcriptional response. CRC patient datasets (TCGA) were used to estimate ATF6 activity and validate ATF6-driven signatures. To investigate the impact of ATF6 signalling on metabolites, untargeted metabolomics of faeces and targeted lipidomics of tissue were performed. Mucosal microbiota was spatially characterised by 16S rRNA profiling at mm resolution along the colonic longitudinal axis. Based on 16S rRNA data, Phylogenetic Investigation of Communities Reconstruction of Unobserved States (PICRUSt2) was used to infer microbiota lipid-specific functional content. Results We identified an ATF6-UPR core of 368 differentially expressed genes fully activated by acute ATF6 signalling. Functional analysis using KEGG pathways showed that chronic ATF6 signalling predominantly alters UPR-related and metabolic pathways, with 22% of metabolic pathway genes classified as lipid metabolism. GF mice confirmed that the microbiota enhances ATF6-induced metabolic changes. Kaplan-Meier analyses significantly associate our microbiota-dependent ATF6-driven and lipid-specific ATF6-driven gene signatures with decreased disease-free survival in CRC patients since primary therapy. Moreover, ATF6 activity correlates with the presence of CRC-associated bacteria in TCGA samples. Tumor-susceptible mice show alterations in lipid metabolites, particularly long-chain fatty acids (FA) and elongation of saturated FA. PICRUSt2 revealed bacterial lipid detoxification mechanisms, with an increased total abundance of oleate hydratase-positive species. Conclusion Chronic ATF6-signalling alters host lipid metabolism and the lipid milieu in tumor-developing nATF6IEC mice. ATF6-driven microbiota changes are concomitant with bacterial lipid detoxification mechanisms in the tumor niche. We postulate that chronic ATF6 signalling represents a clinically relevant pathologic response that alters the intestinal lipid milieu and thus selects for a tumor-promoting microbiota.
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Warinner, James, Mohamed ElSaadani, Kian Rosenau, Jong Hyun Kim, Syed Adeel Hassan, Sarayu Bhogoju, Lesley Wempe, et al. "AUPHOS, A NOVEL DRUG THAT IMPROVES COLITIS BY MICROBIOME INDUCED METABOLIC CHANGES." Inflammatory Bowel Diseases 29, Supplement_1 (January 26, 2023): S49. http://dx.doi.org/10.1093/ibd/izac247.094.
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Abstract BACKGROUND Dysbiotic intestinal microbiomes dominated by facultative anaerobes are strongly associated with inflammatory bowel disease (IBD). More recently, data from Baumler and colleagues support a model where mitochondrial dysfunction causes disease-associated dysbiosis by increasing oxygen (O2) availability to the microbiome. We posit that the restoration of epithelial mitochondrial respiration contributes to the restoration of a healthy microbiome dominated by facultative anaerobes such as Firmicutes [that produce short chain fatty acids (SCFA)]. Here, we tested a novel compound (AuPhos) that increases an O2 consumption in intestinal epithelial cells (IECs) thereby reducing O2 availability to the microbiome and promotes a healthy anaerobic environment (and blooms of firmicutes). METHOD Inbred C57BL/6 mice (n=3) were given oral vehicle (0.5% DMSO/Tween-80) or AuPhos (2.5 or 25mg/Kg;q3d) for two weeks, and colon and stool samples were extracted at day-15 sacrifice. Microbial DNA was isolated from stool samples using PoweFecal kit followed by 16S rRNA metagenomic sequencing. Linear Discriminant Analysis (LDA) and PICRUST2 were performed to reveal differentially abundant bacterial species and functional potentials of bacterial communities, respectively. Similar microbial profiling was performed on AuPhos-fed acute colitis mice (2% DSS-7d; Recovery-16d). Effect of AuPhos on microbial metabolism was determined by 1H NMR for detecting SCFA synthesis by gut microbiota in stool samples (n=3) collected after 3 consecutive doses. AuPhos-induced hypoxia in IECs was assessed by Hypoxyprobe-1 kit. RESULT Metagenomic analysis showed reduction in relative abundance of (O2 consuming) Proteobacteria and facultatively anaerobic Enterobacteriaceae in the gut, in AuPhos-fed mice. Conversely, AuPhos treatment dose- dependently increased the relative abundance of signature anaerobic bacteria e.g. Firmicutes including Clostridia (Faecalibacterium prausnitzii, Roseburia sp.), Bifidobacterium, etc. PICRUST2 and LDA revealed that AuPhos decreased bacterial LPS biosynthetic pathway and increased overall fatty acid biosynthesis pathways. AuPhos increased butyrate and propionate levels by >35% and acetate by 60% (n=3) compared to stools from vehicle-treated mice. In DSS-colitis mice, AuPhos reduced the relative abundance of inflammatory Proteobacteria, which includes facultative anaerobic Enterobacteriaceae family and increased Firmicutes over time (p<0.05). Interestingly, hypoxia staining showed AuPhos-induced O2 utilization in colonic surface IECs, facilitating obligate anaerobe-promoting environment in the gut. CONCLUSION These finding suggest that AuPhos is a “first-in-class” oral therapeutic that has a potential to correct microbial dysbiosis in IBD by reducing epithelial oxygenation and thereby promoting a healthy microbiome dominated by obligate anaerobes.
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Yuan, Huatao, Tangcheng Li, Hongfei Li, Cong Wang, Ling Li, Xin Lin, and Senjie Lin. "Diversity Distribution, Driving Factors and Assembly Mechanisms of Free-Living and Particle-Associated Bacterial Communities at a Subtropical Marginal Sea." Microorganisms 9, no. 12 (November 27, 2021): 2445. http://dx.doi.org/10.3390/microorganisms9122445.
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Free-living (FL) and particle-associated (PA) bacterioplankton communities play critical roles in biogeochemical cycles in the ocean. However, their community composition, assembly process and functions in the continental shelf and slope regions are poorly understood. Based on 16S rRNA gene amplicon sequencing, we investigated bacterial communities’ driving factors, assembly processes and functional potentials at a subtropical marginal sea. The bacterioplankton community showed specific distribution patterns with respect to lifestyle (free living vs. particle associated), habitat (slope vs. shelf) and depth (surface vs. DCM and Bottom). Salinity and water temperature were the key factors modulating turnover in the FL community, whereas nitrite, silicate and phosphate were the key factors for the PA community. Model analyses revealed that stochastic processes outweighed deterministic processes and had stronger influences on PA than FL. Homogeneous selection (Hos) was more responsible for the assembly and turnover of FL, while drift and dispersal limitation contributed more to the assembly of PA. Importantly, the primary contributor to Hos in PA was Gammaproteobacteria:Others, whereas that in FL was Cyanobacteria:Bin6. Finally, the PICRUSt2 analysis indicated that the potential metabolisms of carbohydrates, cofactors, amino acids, terpenoids, polyketides, lipids and antibiotic resistance were markedly enriched in PA than FL.
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Yasuda, Michiko, Khondoker M. G. Dastogeer, Elsie Sarkodee-Addo, Chihiro Tokiwa, Tsuyoshi Isawa, Satoshi Shinozaki, and Shin Okazaki. "Impact of Azospirillum sp. B510 on the Rhizosphere Microbiome of Rice under Field Conditions." Agronomy 12, no. 6 (June 5, 2022): 1367. http://dx.doi.org/10.3390/agronomy12061367.
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There has been increasing attention toward the influence of biofertilizers on the composition of microbial communities associated with crop plants. We investigated the impact of Azospirillum sp. B510, a bacterial strain with nitrogen-fixing ability, on the structure of bacterial and fungal communities within rice plant rhizospheres by amplicon sequencing at two sampling stages (the vegetative and harvest stages of rice). Principal coordinate analysis (PCoA) demonstrated a significant community shift in the bacterial microbiome when the plants were inoculated with B510 at the vegetative stage, which was very similar to the effect of chemical N-fertilizer application. This result suggested that the inoculation with B510 strongly influenced nitrogen uptake by the host plants under low nitrogen conditions. Least discriminant analysis (LDA) showed that the B510 inoculation significantly increased the N2-fixing Clostridium, Aeromonas and Bacillus populations. In contrast, there was no apparent influence of B510 on the fungal community structure. The putative functional properties of bacteria were identified through PICRUSt2, and this hinted that amino acid, sugar and vitamin production might be related to B510 inoculation. Our results indicate that B510 inoculation influenced the bacterial community structure by recruiting other N2-fixing bacteria in the absence of nitrogen fertilizer.
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Yuan, Xiangqun, Xuan Zhang, Xueying Liu, Yanlu Dong, Zizheng Yan, Dongbiao Lv, Ping Wang, and Yiping Li. "Comparison of Gut Bacterial Communities of Grapholita molesta (Lepidoptera: Tortricidae) Reared on Different Host Plants." International Journal of Molecular Sciences 22, no. 13 (June 25, 2021): 6843. http://dx.doi.org/10.3390/ijms22136843.
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Intestinal symbiotic bacteria have played an important role in the digestion, immunity detoxification, mating, and reproduction of insects during long-term coevolution. The oriental fruit moth, Grapholita molesta, is an important fruit tree pest worldwide. However, the composition of the G. molesta microbial community, especially of the gut microbiome, remains unclear. To explore the differences of gut microbiota of G. molesta when reared on different host plants, we determined the gut bacterial structure when G. molesta was transferred from an artificial diet to different host plants (apples, peaches, nectarines, crisp pears, plums, peach shoots) by amplicon sequencing technology. The results showed that Proteobacteria and Firmicutes are dominant in the gut microbiota of G. molesta. Plum-feeding G. molesta had the highest richness and diversity of gut microbiota, while apple-feeding G. molesta had the lowest. PCoA and PERMANOVA analysis revealed that there were significant differences in the gut microbiota structure of G. molesta on different diets. PICRUSt2 analysis indicated that most of the functional prediction pathways were concentrated in metabolic and cellular processes. Our results confirmed that gut bacterial communities of G. molesta can be influenced by host diets and may play an important role in host adaptation.