A total crapshoot? Evaluating bioinformatic decisions in animal diet metabarcoding analyses

Ecology and Evolution, Journal Year: 2020, Volume and Issue: 10(18), P. 9721 - 9739

Published: July 23, 2020

Abstract Metabarcoding studies provide a powerful approach to estimate the diversity and abundance of organisms in mixed communities nature. While strategies exist for optimizing sample sequence library preparation, best practices bioinformatic processing amplicon data are lacking animal diet studies. Here we evaluate how decisions made core processes, including filtering, database design, classification, can influence metabarcoding results. We show that denoising methods have lower error rates compared traditional clustering methods, although these differences largely mitigated by removing low‐abundance variants. also found available reference datasets from GenBank BOLD marker gene cytochrome oxidase I (COI) be complementary, discuss improve existing databases include versioned releases. Taxonomic classification dramatically affect For example, commonly used Barcode Life Database (BOLD) Classification API assigned fewer names samples order through species levels using both mock community bat guano all other classifiers (vsearch‐SINTAX q2‐feature‐classifier's BLAST + LCA, VSEARCH Naive Bayes classifiers). The lack consensus on bioinformatics limits comparisons among may introduce biases. Our work suggests biological offer useful standard myriad computational impacting accuracy. Further, highlight need continual evaluations as new tools adopted ensure inferences drawn reflect meaningful biology instead digital artifacts.

Language: Английский

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Remodeling of the maternal gut microbiome during pregnancy is shaped by parity

Microbiome, Journal Year: 2021, Volume and Issue: 9(1)

Published: June 27, 2021

Abstract Background The maternal microbiome has emerged as an important factor in gestational health and outcome is associated with risk of preterm birth offspring morbidity. Epidemiological evidence also points to successive pregnancies—referred parity—as a for birth, infant mortality, impaired neonatal growth. Despite the fact that both parity are linked maternal-infant health, impact on remains largely unexplored, part due challenges studying humans. Results Using synchronized pregnancies dense longitudinal monitoring pigs, we describe trajectory during pregnancy determine extent which modulates this trajectory. We show changes reproducibly gestation remodeling occurs more rapidly increases. At time parturition, was relative abundance several bacterial species, including Treponema bryantii , Lactobacillus amylovorus reuteri . Strain tracking carried out 18 maternal-offspring “quadrads”—each consisting one mother sow three piglets—linked altered levels Akkermansia muciniphila, Prevotella stercorea, Campylobacter coli gut 10 days after birth. Conclusions Collectively, these results identify environmental highlight utility swine model investigating health. In addition, our data extends beyond alterations community bacteria colonize early life. species identified parity-associated have been shown influence host metabolism other systems, raising possibility such may nutrient acquisition or utilization. These findings, taken together observation even subtle differences changes, underscore importance considering design analysis human studies infants.

Language: Английский

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Reduced B12 uptake and increased gastrointestinal formate are associated with archaeome-mediated breath methane emission in humans

Microbiome, Journal Year: 2021, Volume and Issue: 9(1)

Published: Sept. 24, 2021

Methane is an end product of microbial fermentation in the human gastrointestinal tract. This gas solely produced by archaeal subpopulation microbiome. Increased methane production has been associated with abdominal pain, bloating, constipation, IBD, CRC or other conditions. Twenty percent (healthy) Western populations innately exhale substantially higher amounts (>5 ppm) this gas. The underlying principle for differential emission and its effect on health not sufficiently understood.We assessed breath content, microbiome, function metabolome, dietary intake one-hundred healthy young adults (female: n = 52, male: 48; mean age =24.1). On basis amount emitted, participants were grouped into high emitters (CH4 content 5-75 low < 5 ppm). microbiomes characterized a 1000-fold increase Methanobrevibacter smithii. archaeon co-occurred bacterial community specialized fibre degradation, which included members Ruminococcaceae Christensenellaceae. As confirmed metagenomics metabolomics, biology producers was further increased formate acetate levels gut. These metabolites strongly correlated habits, such as vitamin, fat intake, microbiome function, altogether driving methanogenesis.This study enlightens complex, multi-level interplay host diet, genetics composition/function leading to two fundamentally different phenotypes identifies novel points therapeutic action methane-associated disorders. Video Abstract.

Language: Английский

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Evaluation of the Effect of Storage Methods on Fecal, Saliva, and Skin Microbiome Composition

mSystems, Journal Year: 2021, Volume and Issue: 6(2)

Published: April 27, 2021

As the number of human microbiome studies expand, it is increasingly important to identify cost-effective, practical preservatives that allow for room temperature sample storage. Here, we reanalyzed 16S rRNA gene amplicon sequencing data from a large storage study published in 2016 and performed shotgun metagenomic on remnant DNA this experiment. Both results support initial findings 95% ethanol, nontoxic, cost-effective preservative, effective at preserving samples weeks. We expanded analysis by collecting new set fecal, saliva, skin determine optimal ratio ethanol sample. identified collection protocols fecal (storing swab ethanol) saliva unstimulated 1:2). Storing swabs reduced microbial biomass disrupted community composition, highlighting difficulties low preservation. The solutions large-scale analyses oral communities.IMPORTANCE Expanding our knowledge communities across diverse environments includes places far laboratory. Identifying will enable crucial enabling populations. validate efficiently preserves composition also stool preserve both load composition. These provide rationale an accessible, solution crowdsourcing studies, such as Microsetta Initiative, lower barrier samples.

Language: Английский

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Composition and Associations of the Infant Gut Fungal Microbiota with Environmental Factors and Childhood Allergic Outcomes

mBio, Journal Year: 2021, Volume and Issue: 12(3)

Published: June 11, 2021

Recent evidence suggests an immunomodulatory role for commensal fungi (mycobiota) in the gut, yet little is known about composition and dynamics of early-life gut fungal communities. In this work, we show first time that mycobiota Canadian infants changes dramatically over course year life, associated with environmental factors such as geographical location, diet, season birth, can be used conjunction knowledge a small number key to predict inhalant atopy status at age 5 years.

Language: Английский

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