scholarly journals Evaluating bacterial and functional diversity of human gut microbiota by complementary metagenomics and metatranscriptomics

2018 ◽  
Author(s):  
Ravi Ranjan ◽  
Asha Rani ◽  
Patricia W. Finn ◽  
David L. Perkins
Keyword(s):  
Gut Microbiota ◽  
Sequence Data ◽  
Bacterial Species ◽  
Abundant Species ◽  
Shotgun Sequencing ◽  
Sequencing Data ◽  
Illumina Platform ◽  
Shotgun Metagenomics ◽  
Differential Gene ◽  
Detectable Bias

ABSTRACTIt is well accepted that dysbiosis of microbiota is associated with disease; however, the biological mechanisms that promote susceptibility or resilience to disease remain elusive. One of the major limitations of previous microbiome studies has been the lack of complementary metatranscriptomic (functional) data to complement the interpretation of metagenomics (bacterial abundance). The purpose of the study was twofold, first to evaluate the bacterial diversity and differential gene expression of gut microbiota using complementary shotgun metagenomics (MG) and metatranscriptomics (MT) from same fecal sample. Second, to compare sequence data using different Illumina platforms and with different sequencing parameters as new sequencers are introduced and determine if the data are comparable on different platforms. In this study, we perform ultra-deep metatranscriptomic shotgun sequencing for a sample that we previously analyzed with metagenomics shotgun sequencing. We validated the sequencing and analysis methods using different Illumina platform, and with different sequencing and analysis parameters. Our results suggest that use of different Illumina platform did not lead to detectable bias in the sequencing data. The analysis of the sample using MG and MT approach shows that some species genes are more highly represented in the MT than in the MG, indicating that some species are highly metabolically active. Our analysis also shows that ~52% of the genes in the metagenome are in the metatranscriptome, and therefore are robustly expressed. The functions of the low and rare abundance bacterial species remain poorly understood. Our observations indicate that among the low abundant species analyzed in this study some were found to be more metabolically active compared to others and can contribute distinct profiles of biological functions that may modulate the host-microbiota and bacteria-bacteria interactions.

scholarly journals Multiomic Strategies Reveal Diversity and Important Functional Aspects of Human Gut Microbiome

2018 ◽  
Vol 2018 ◽  
pp. 1-13 ◽  
Author(s):  
Ravi Ranjan ◽  
Asha Rani ◽  
Patricia W. Finn ◽  
David L. Perkins
Keyword(s):  
Sequence Data ◽  
Bacterial Species ◽  
Abundant Species ◽  
Shotgun Sequencing ◽  
Sequencing Analysis ◽  
Sequencing Data ◽  
Illumina Platform ◽  
Shotgun Metagenomics ◽  
Functional Aspects ◽  
Detectable Bias

It is well accepted that dysbiosis of microbiota is associated with disease; however, the biological mechanisms that promote susceptibility or resilience to disease remain elusive. One of the major limitations of previous microbiome studies has been the lack of complementary metatranscriptomic (functional) data to complement the interpretation of metagenomics (bacterial abundance). The purpose of this study was twofold, first to evaluate the bacterial diversity and differential gene expression of gut microbiota using complementary shotgun metagenomics (MG) and metatranscriptomics (MT) from same fecal sample. Second, to compare sequence data using different Illumina platforms and with different sequencing parameters as new sequencers are introduced, and to determine if the data are comparable on different platforms. In this study, we perform ultradeep metatranscriptomic shotgun sequencing for a sample that we previously analyzed with metagenomics shotgun sequencing. We performed sequencing analysis using different Illumina platforms, with different sequencing and analysis parameters. Our results suggest that use of different Illumina platform did not lead to detectable bias in the sequencing data. The analysis of the sample using MG and MT approach shows that some species genes are highly represented in the MT than in the MG, indicating that some species are highly metabolically active. Our analysis also shows that ~52% of the genes in the metagenome are in the metatranscriptome and therefore are robustly expressed. The functions of the low and rare abundance bacterial species remain poorly understood. Our observations indicate that among the low abundant species analyzed in this study some were found to be more metabolically active compared to others, and can contribute distinct profiles of biological functions that may modulate the host-microbiota and bacteria-bacteria interactions.

scholarly journals Inferring species compositions of complex fungal communities from long- and short-read sequence data

2021 ◽  
Author(s):  
Yiheng Hu ◽  
Laszlo Irinyi ◽  
Minh Thuy Vi Hoang ◽  
Tavish Eenjes ◽  
Abigail Graetz ◽  
...  
Keyword(s):  
Community Composition ◽  
Pathogen Detection ◽  
High Throughput Sequencing ◽  
Sequence Data ◽  
Whole Genome Sequence ◽  
Composition Analysis ◽  
Sequencing Data ◽  
Species Classification ◽  
Shotgun Metagenomics ◽  
Query Coverage

Background: The kingdom fungi is crucial for life on earth and is highly diverse. Yet fungi are challenging to characterize. They can be difficult to culture and may be morphologically indistinct in culture. They can have complex genomes of over 1 Gb in size and are still underrepresented in whole genome sequence databases. Overall their description and analysis lags far behind other microbes such as bacteria. At the same time, classification of species via high throughput sequencing without prior purification is increasingly becoming the norm for pathogen detection, microbiome studies, and environmental monitoring. However, standardized procedures for characterizing unknown fungi from complex sequencing data have not yet been established. Results: We compared different metagenomics sequencing and analysis strategies for the identification of fungal species. Using two fungal mock communities of 44 phylogenetically diverse species, we compared species classification and community composition analysis pipelines using shotgun metagenomics and amplicon sequencing data generated from both short and long read sequencing technologies. We show that regardless of the sequencing methodology used, the highest accuracy of species identification was achieved by sequence alignment against a fungi-specific database. During the assessment of classification algorithms, we found that applying cut-offs to the query coverage of each read or contig significantly improved the classification accuracy and community composition analysis without significant data loss. Conclusion: Overall, our study expands the toolkit for identifying fungi by improving sequence-based fungal classification, and provides a practical guide for the design of metagenomics analyses.

scholarly journals Metaproteomics Analysis Reveals the Adaptation Process for the Chicken Gut Microbiota

2013 ◽  
Vol 80 (2) ◽  
pp. 478-485 ◽  
Author(s):  
Yue Tang ◽  
Anthony Underwood ◽  
Adriana Gielbert ◽  
Martin J. Woodward ◽  
Liljana Petrovska
Keyword(s):  
16S Rrna ◽  
Gut Microbiota ◽  
High Throughput Sequencing ◽  
Bacterial Species ◽  
Abundant Species ◽  
Fecal Microbiota ◽  
Rrna Gene ◽  
Sequencing Analysis ◽  
Content Type ◽  
Chicken Gut Microbiota

ABSTRACTThe animal gastrointestinal tract houses a large microbial community, the gut microbiota, that confers many benefits to its host, such as protection from pathogens and provision of essential metabolites. Metagenomic approaches have defined the chicken fecal microbiota in other studies, but here, we wished to assess the correlation between the metagenome and the bacterial proteome in order to better understand the healthy chicken gut microbiota. Here, we performed high-throughput sequencing of 16S rRNA gene amplicons and metaproteomics analysis of fecal samples to determine microbial gut composition and protein expression. 16 rRNA gene sequencing analysis identifiedClostridiales,Bacteroidaceae, andLactobacillaceaespecies as the most abundant species in the gut. For metaproteomics analysis, peptides were generated by using the Fasp method and subsequently fractionated by strong anion exchanges. Metaproteomics analysis identified 3,673 proteins. Among the most frequently identified proteins, 380 proteins belonged toLactobacillusspp., 155 belonged toClostridiumspp., and 66 belonged toStreptococcusspp. The most frequently identified proteins were heat shock chaperones, including 349 GroEL proteins, from many bacterial species, whereas the most abundant enzymes were pyruvate kinases, as judged by the number of peptides identified per protein (spectral counting). Gene ontology and KEGG pathway analyses revealed the functions and locations of the identified proteins. The findings of both metaproteomics and 16S rRNA sequencing analyses are discussed.

scholarly journals Switching on the light: using metagenomic shotgun sequencing to characterize the intestinal microbiome of Atlantic cod

2019 ◽  
Author(s):  
Even Sannes Riiser ◽  
Thomas H.A. Haverkamp ◽  
Srinidhi Varadharajan ◽  
Ørnulf Borgan ◽  
Kjetill S. Jakobsen ◽  
...  
Keyword(s):  
Gadus Morhua ◽  
Atlantic Cod ◽  
North Atlantic Ocean ◽  
Bacterial Species ◽  
Abundant Species ◽  
Shotgun Sequencing ◽  
Intestinal Microbiome ◽  
Geographical Differences ◽  
Important Species ◽  
The North

AbstractThe biological roles of the intestinal microbiome and how it is impacted by environmental factors are yet to be determined in wild marine fish species. Atlantic cod (Gadus morhua) is an ecologically important species with a wide-spread distribution in the North Atlantic Ocean. 16S rRNA-based amplicon analyses found no geographical differentiation between the intestinal microbiome of Atlantic cod from different locations. Nevertheless, it is unclear if this lack of differentiation results from an insufficient resolution of this method to resolve fine-scaled biological complexity. Here, we take advantage of the increased resolution provided by metagenomic shotgun sequencing to investigate the intestinal microbiome of 19 adult Atlantic cod individuals from two coastal populations in Norway – located 470 km apart. Our results show that the intestinal microbiome is dominated by theVibrionalesorder, consisting of varying abundances ofPhotobacterium, AliivibrioandVibriospecies. Moreover, resolving the species community to unprecedented resolution, we identify two abundant species,P. iliopiscariumandP. kishitanii,which comprise over 50% of the classified reads. Interestingly, genomic data shows that the intestinalP. kishitaniistrains have functionally intactluxgenes, and its high abundance suggests that fish intestines form an important part of its ecological niche. These observations support a hypothesis that bioluminescence plays an ecological role in the marine food web. Despite our improved taxonomical resolution, we identify no geographical differences in bacterial community structure, indicating that the intestinal microbiome of these coastal cod is colonized by a limited number of closely related bacterial species with a broad geographical distribution that are well suited to thrive in this host-associated environment.

scholarly journals Deep Investigating the Changes of Gut Microbiome and Its Correlation With the Shifts of Host Serum Metabolome Around Parturition in Sows

2021 ◽  
Vol 12 ◽  
Author(s):  
Hao Fu ◽  
Maozhang He ◽  
Jinyuan Wu ◽  
Yunyan Zhou ◽  
Shanlin Ke ◽  
...  
Keyword(s):  
16S Rrna ◽  
Gut Microbiota ◽  
16S Rrna Gene ◽  
Gut Microbiome ◽  
Bacterial Species ◽  
Late Pregnancy ◽  
Rrna Gene ◽  
Metagenomic Sequencing ◽  
Sequencing Data ◽  
Functional Capacities

Parturition is a crucial event in the sow reproduction cycle, which accompanies by a series of physiological changes, including sex hormones, metabolism, and immunity. More and more studies have indicated the changes of the gut microbiota from pregnancy to parturition. However, what bacterial species and functional capacities of the gut microbiome are changed around parturition has been largely unknown, and the correlations between the changes of gut bacterial species and host metabolome were also uncovered. In this study, by combining 16S rRNA gene and shotgun metagenomic sequencing data, and the profiles of serum metabolome and fecal short-chain fatty acids (SCFAs), we investigated the changes of gut microbiome, serum metabolite features and fecal SCFAs from late pregnancy (LP) to postpartum (PO) stage. We found the significant changes of gut microbiota from LP to PO stage in both 16S rRNA gene sequencing and metagenomic sequencing analyses. The bacterial species from Lactobacillus, Streptococcus, and Clostridium were enriched at the LP stage, while the species from Bacteroides, Escherichia, and Campylobacter had higher abundances at the PO stage. Functional capacities of the gut microbiome were also significantly changed and associated with the shifts of gut bacteria. Untargeted metabolomic analyses revealed that the metabolite features related to taurine and hypotaurine metabolism, and arginine biosynthesis and metabolism were enriched at the LP stage, and positively associated with those bacterial species enriched at the LP stage, while the metabolite features associated with vitamin B6 and glycerophospholipid metabolism had higher abundances at the PO stage and were positively correlated with the bacteria enriched at the PO stage. Six kinds of SCFAs were measured in feces samples and showed higher concentrations at the LP stage. These results suggested that the changes of gut microbiome from LP to PO stage lead to the shifts of host lipid, amino acids and vitamin metabolism and SCFA production. The results from this study provided new insights for the changes of sow gut microbiome and host metabolism around parturition, and gave new knowledge for guiding the feeding and maternal care of sows from late pregnancy to lactation in the pig industry.

scholarly journals MALT: Fast alignment and analysis of metagenomic DNA sequence data applied to the Tyrolean Iceman

2016 ◽  
Author(s):  
Alexander Herbig ◽  
Frank Maixner ◽  
Kirsten I. Bos ◽  
Albert Zink ◽  
Johannes Krause ◽  
...  
Keyword(s):  
Large Scale ◽  
Sequence Data ◽  
Bacterial Species ◽  
Human Microbiome ◽  
Metagenomic Analysis ◽  
Sequencing Data ◽  
Metagenomic Dna ◽  
Alignment Procedure ◽  
Taxonomic Profile ◽  
Tyrolean Iceman

AbstractModern next generation sequencing technologies produce vast amounts of data in the context of large-scale metagenomic studies, in which complex microbial communities can be reconstructed to an unprecedented level of detail. Most prominent examples are human microbiome studies that correlate the bacterial taxonomic profile with specific physiological conditions or diseases.In order to perform these analyses high-throughput computational tools are needed that are able to process these data within a short time while preserving a high level of sensitivity and specificity.Here we present MALT (MEGAN ALignment Tool) a program for the ultrafast alignment and analysis of metagenomic DNA sequencing data. MALT processes hundreds of millions of sequencing reads within only a few hours. In addition to the alignment procedure MALT implements a taxonomic binning algorithm that is able to specifically assign reads to bacterial species. Its tight integration with the interactive metagenomic analysis software MEGAN allows for visualization and further analyses of results.We demonstrate MALT by its application to the metagenomic analysis of two ancient microbiomes from oral cavity and lung samples of the 5,300-year-old Tyrolean Iceman. Despite the strong environmental background, MALT is able to pick up the weak signal of the original microbiomes and identifies multiple species that are typical representatives of the respective host environment.

scholarly journals Dietary factors, gut microbiota, and serum trimethylamine-N-oxide associated with cardiovascular disease

2020 ◽  
Author(s):  
Zhendong Mei ◽  
Guo-Chong Chen ◽  
Zheng Wang ◽  
Mykhaylo Usyk ◽  
Bing Yu ◽  
...  
Keyword(s):  
Cardiovascular Disease ◽  
Gut Microbiota ◽  
Multiple Testing ◽  
Bacterial Species ◽  
Positive Association ◽  
Red Meat ◽  
Dietary Factors ◽  
Health Study ◽  
Multiple Testing Correction ◽  
Shotgun Metagenomics

Abstract Background Trimethylamine-N-oxide (TMAO), a diet-derived and gut microbiota-related metabolite, is associated with cardiovascular disease (CVD). However, the major dietary determinants and the specific gut bacterial taxa related to TMAO remain to be identified in humans. We aimed to identify dietary and gut microbial factors independently and jointly associated with circulating TMAO. Results We examined usual dietary intake, fecal gut microbiome profiled by shotgun metagenomics, and their interactions in relation to serum TMAO and its precursors among up to 3972 adult participants from the Hispanic Community Health Study/Study of Latinos. We confirmed the positive association between TMAO and prevalent CVD (OR = 1.28, P = 4.36⋅10− 4). Fish (P = 1.26⋅10− 17), red meat (P = 3.33⋅10− 16), and egg (P = 3.89⋅10− 5) intakes were top dietary factors positively associated with serum TMAO independently of each other. Red meat and egg intakes, but not fish intake, were positively associated with serum TMAO precursors (e.g., carnitine, choline). We identified 9 gut bacterial species significantly associated with serum TMAO after multiple testing correction (FDR < 0.05). All 4 TMAO-positively-associated bacteria belong to the Clostridiales order, 3 of which may have homologous genes encoding carnitine monooxygenase, an enzyme converting carnitine to trimethylamine (TMA)/TMAO. The red meat-TMAO association was more pronounced for participants with higher abundance of these 4 bacterial species than those with lower abundance (Pinteraction=0.013), but such microbial modification was not observed for fish-TMAO or egg-TMAO associations. Conclusion In US Hispanics/Latinos, fish, red meat, and egg intakes are major dietary factors associated with serum TMAO. The identified potential TMA-producing gut microbiota and microbial modification on the red meat-TMAO association support microbial TMA/TMAO production from dietary carnitine, while the fish-TMAO association is independent of gut microbiota.

scholarly journals Streaming algorithms for identification of pathogens and antibiotic resistance potential from real-time MinIONTM sequencing

2015 ◽  
Author(s):  
Minh Duc Cao ◽  
Devika Ganesamoorthy ◽  
Alysha G. Elliott ◽  
Huihui Zhang ◽  
Matthew A. Cooper ◽  
...  
Keyword(s):  
Drug Resistance ◽  
Antibiotic Resistance ◽  
Real Time ◽  
Sequence Data ◽  
Bacterial Species ◽  
Strain Typing ◽  
Streaming Algorithms ◽  
Sequencing Data ◽  
Desktop Computer ◽  
Antibiotic Resistance Profile

AbstractThe recently introduced Oxford Nanopore MinION platform generates DNA sequence data in real-time. This opens immense potential to shorten the sample-to-results time and is likely to lead to enormous benefits in rapid diagnosis of bacterial infection and identification of drug resistance. However, there are very few tools available for streaming analysis of real-time sequencing data. Here, we present a framework for streaming analysis of MinION real-time sequence data, together with probabilistic streaming algorithms for species typing, multi-locus strain typing, gene presence strain-typing and antibiotic resistance profile identification. Using three culture isolate samples as well as a mixed-species sample, we demonstrate that bacterial species and strain information can be obtained within 30 minutes of sequencing and using about 500 reads, initial drug-resistance profiles within two hours, and complete resistance profiles within 10 hours. Multi-locus strain typing required more than 15x coverage to generate confident assignments, whereas gene-presence typing could detect the presence of a known strain with 0.5x coverage. We also show that our pipeline can process over 100 times more data than the current throughput of the MinION on a desktop computer.

scholarly journals Berberine May Correct Corticosteroid Resistance Induced By Gut Microbiota Dysbiosis in Immune Thrombocytopenia

Blood ◽  
2018 ◽  
Vol 132 (Supplement 1) ◽  
pp. 3769-3769 ◽  
Author(s):  
Ya-Nan Wang ◽  
Xiao Liu ◽  
Yun He ◽  
Qian-Ming Wang ◽  
Xiao-Lu Zhu ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Corticosteroid Therapy ◽  
Gut Microbiome ◽  
Immune Thrombocytopenia ◽  
Shotgun Sequencing ◽  
Healthy Controls ◽  
Sequencing Data ◽  
Corticosteroid Resistance ◽  
Gut Microbiota Dysbiosis ◽  
Microbiota Structure

Abstract Introduction Immune thrombocytopenia (ITP) is an autoimmune disorder characterized by abnormal immune response. Though many therapies have been used, corticosteroid-resistance remains to be a challenge clinically. Extensive research has improved our understanding of ITP, showing that environmental factors affect the disease profile, such as Helicobacter pylori being proven to be associated with thrombocytopenia. Though evidence that the gut microbiota contributes to the development of auto-immune disorders is accumulating, there is no information available on relationship between gut microbiome and ITP. Berberine(BBR), a traditional compound isolated from a Chinese herb, has been widely used as a nonprescription drug to treat diarrhea. Recently, BBR has been reported to modulate microbiota structures, which contributes to improving metabolic disorders. Here, we hypothesized that BBR might modulate gut microbiota to treat ITP. Methods In order to investigate the relationship between gut microbiome and ITP, we performed deep shotgun sequencing on 253 fecal samples totally from consecutive ITP patients and healthy controls. Metagenome-wide association study (MWAS) was conducted, and clinical characteristics of patients were collected to analyze the correlation with gut microbiome (Nan Qin, et al. Nature. 2012). Certainly, a clinical cohort study was performed to assess the efficacy of BBR in corticosteroid-resistant ITP patients. To better characterize the role of gut microbiota in the development of ITP and to verify the modulating effect of BBR on gut microbiota structure, we performed colonization of mice with specific bacterium and established active murine models (immunized-splenocyte engraftment) of BBR treatment. Result We integrated the sequencing data into an existing gut microbial reference-gene catalog and identified 35275 genes that differ in abundance between ITP patients and healthy controls. We then clustered the genes into metagenomic species (MGS) and finally identified 15 MGS which were significantly different in both discovery cohort and validation cohort. Dysbiosis was detected in the gut microbiome of ITP patients, as both phylogenetic analysis and MGS annotation indicated that Lachnospiraceae bacterium, Clostridium asparagiforme were over-represented while Bacteroides spp was depleted in ITP patients comparing with healthy controls. Functionally, KEGG annotation showed that the most enriched orthologs in ITP patients were related to membrane transport. Moreover, the biosynthesis of microbe-associated molecular patterns (MAMPs) such as lipopolysaccharides (LPS), peptidoglycan biosynthesis and flagellin were highly abundant in patients. Gene biomarkers and cluster markers based on gut microbiome were established to identify ITP patients and were validated in an independent cohort. The alterations of gut microbiome in ITP patients are partly reversed after treatment. Furthermore, L. bacterium shows more abundant in corticosteroid-resistant ITP comparing with newly diagnosed ITP. Specifically, BBR treatment could improve the microbial dysbiosis of corticosteroid-resistant ITP patients, the complete response (CR), response(R), and overall response (OR) rates being 26.3%, 47.4% and 73.7%, respectively. Targeted QPCR assay determined that L. bacterium accumulated in corticosteroid-resistant ITP, consistent with the result of shotgun sequencing data. Gavage with L. bacterium results in significantly alterations of gut microbiota structure in mice comparing with mice without bacterial administration or those receiving Clostridium asparagiforme administration. Moreover, colonization of L. bacterium caused more severe thrombocytopenia and impaired the response to corticosteroid therapy in active ITP model. Intriguingly, BBR treatment, but not any other antibiotics, could reverse the effect of L. bacterium colonization on gut microbiota structure and enhance the response to corticosteroid therapy. Conclusion Our findings demonstrate that the gut microbiome alters in ITP and is partly normalized after treatment. Gut microbiota dysbiosis may contribute to the development of corticosteroid-resistant ITP. BBR may correct corticosteroid-resistance by modulating the gut microbiota structure, thus being a novel potential second-line candidate to treat ITP. Disclosures No relevant conflicts of interest to declare.

Understanding the gut–kidney axis in nephrolithiasis: an analysis of the gut microbiota composition and functionality of stone formers

Gut ◽  
2018 ◽  
Vol 67 (12) ◽  
pp. 2097-2106 ◽  
Author(s):  
Andrea Ticinesi ◽  
Christian Milani ◽  
Angela Guerra ◽  
Franca Allegri ◽  
Fulvio Lauretani ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Dietary Habits ◽  
Bacterial Species ◽  
Inverse Correlation ◽  
Microbiota Composition ◽  
Shotgun Metagenomics ◽  
Microbial Profiling ◽  
Stone Formers ◽  
Faecal Samples ◽  
Gut Microbiota Composition

ObjectivesThe involvement of the gut microbiota in the pathogenesis of calcium nephrolithiasis has been hypothesised since the discovery of the oxalate-degrading activity of Oxalobacter formigenes, but never comprehensively studied with metagenomics. The aim of this case–control study was to compare the faecal microbiota composition and functionality between recurrent idiopathic calcium stone formers (SFs) and controls.DesignFaecal samples were collected from 52 SFs and 48 controls (mean age 48±11). The microbiota composition was analysed through 16S rRNA microbial profiling approach. Ten samples (five SFs, five controls) were also analysed with deep shotgun metagenomics sequencing, with focus on oxalate-degrading microbial metabolic pathways. Dietary habits, assessed through a food-frequency questionnaire, and 24-hour urinary excretion of prolithogenic and antilithogenic factors, including calcium and oxalate, were compared between SFs and controls, and considered as covariates in the comparison of microbiota profiles.ResultsSFs exhibited lower faecal microbial diversity than controls (Chao1 index 1460±363vs 1658±297, fully adjusted p=0.02 with stepwise backward regression analysis). At multivariate analyses, three taxa (Faecalibacterium, Enterobacter, Dorea) were significantly less represented in faecal samples of SFs. The Oxalobacter abundance was not different between groups. Faecal samples from SFs exhibited a significantly lower bacterial representation of genes involved in oxalate degradation, with inverse correlation with 24-hour oxalate excretion (r=−0.87, p=0.002). The oxalate-degrading genes were represented in several bacterial species, whose cumulative abundance was inversely correlated with oxaluria (r=−0.85, p=0.02).ConclusionsIdiopathic calcium SFs exhibited altered gut microbiota composition and functionality that could contribute to nephrolithiasis physiopathology.

Sign in / Sign up

Export Citation Format

Share Document