Interpretations of Environmental Microbial Community Studies Are Biased by the Selected 16S rRNA (Gene) Amplicon Sequencing Pipeline

Frontiers in Microbiology, Год журнала: 2020, Номер 11

Опубликована: Окт. 23, 2020

One of the major methods to identify microbial community composition, unravel population dynamics, and explore diversity in environmental samples is high-throughput DNA- or RNA-based 16S rRNA (gene) amplicon sequencing combination with bioinformatics analyses. However, focusing on from contrasting habitats, it was not systematically evaluated i.) which analysis provide results that reflect reality most accurately, ii.) how interpretations studies are biased by different iii.) if optimal workflow can be implemented an easy-to-use pipeline. Here, we compared performance tools (i.e. Mothur, QIIME1, QIIME2, MEGAN) using three mock datasets known composition differed quality, species number abundance distribution even uneven), phylogenetic closely related well-separated sequences). Our showed QIIME2 outcompeted all other investigated sequence recovery (>10 times fewer false positives), taxonomic assignments (>22% better F-score) estimates (>5% assessment), suggesting this approach able situ accurately. Further 24 obtained four terrestrial freshwater sites revealed dramatic differences resulting for pipelines at genus level. For instance, river water Sphaerotilus only reported when QIIME1 (8% abundance) Agitococcus (2% 3% abundance, respectively), but both genera remained undetected analyzed Mothur MEGAN. Since these abundant taxa probably have implications important biogeochemical cycles (e.g. nitrate sulfate reduction) sites, their detection semi-quantitative enumeration crucial valid interpretations. A high-performance computing conformant constructed allow FAIR (Findable, Accessible, Interoperable, Re-usable) starting raw files, identified our study. presented should considered future studies, thereby facilitating data substantially, while maximizing reliability confidence analysis.

Язык: Английский

---

Prospects and challenges of implementing DNA metabarcoding for high-throughput insect surveillance

GigaScience, Год журнала: 2019, Номер 8(8)

Опубликована: Июль 30, 2019

Abstract Trap-based surveillance strategies are widely used for monitoring of invasive insect species, aiming to detect newly arrived exotic taxa as well track the population levels established or endemic pests. Where these traps have low specificity and capture non-target species in excess target pests, need extensive specimen sorting identification creates a major diagnostic bottleneck. While recent development standardized molecular diagnostics has partly alleviated this requirement, single per reaction nature methods does not readily scale sheer number insects trapped programmes. Consequently, lists often restricted few high-priority allowing unanticipated avoid detection potentially establish populations. DNA metabarcoding recently emerged method conducting simultaneous, multi-species complex mixed communities may lend itself ideally rapid bulk trap samples. Moreover, high-throughput sequencing platforms could enable multiplexing hundreds diverse samples on flow cell, thereby providing means dramatically up terms both quantity that can be processed concurrently pest targeted. In review literature, we explore how tailored context highlight unique technical regulatory challenges must considered when implementing technologies into sensitive applications.

Язык: Английский

---

Key bacterial taxa and metabolic pathways affecting gut short-chain fatty acid profiles in early life

The ISME Journal, Год журнала: 2021, Номер 15(9), С. 2574 - 2590

Опубликована: Март 15, 2021

Infant gut microbiota development affects the host physiology throughout life, and short-chain fatty acids (SCFAs) are promising key metabolites mediating microbiota-host relationships. Here, we investigated dense longitudinally collected faecal samples from 12 subjects during first 2 years (n = 1048) to identify early life SCFA patterns their relationships with microbiota. Our results revealed three distinct phases of progression in profiles: phase characterised by low acetate high succinate, middle-phase lactate formate late-phase propionate butyrate. Assessment SCFA-microbiota that butyrate is associated increased Clostridiales breastfeeding cessation, diverse personalised assemblage species possessing acetyl-CoA pathway play major roles production. We also found an association between some infant-type bifidobacterial species, human milk oligosaccharides (HMO)-derived fucose substrate for production breastfeeding. identified genes upregulated fucosylated HMO utilisation bifidobacteria. Notably, bifidobacteria showed interspecific intraspecific variation gene repertoires, cross-feeding contributed This study provides insight into relationships, which important step developing strategies modulating lifelong health.

Язык: Английский

---

Metabolic cooperation and spatiotemporal niche partitioning in a kefir microbial community

Nature Microbiology, Год журнала: 2021, Номер 6(2), С. 196 - 208

Опубликована: Янв. 4, 2021

Язык: Английский

---

Effects of Diet versus Gastric Bypass on Metabolic Function in Diabetes

New England Journal of Medicine, Год журнала: 2020, Номер 383(8), С. 721 - 732

Опубликована: Авг. 19, 2020

Some studies have suggested that in people with type 2 diabetes, Roux-en-Y gastric bypass has therapeutic effects on metabolic function are independent of weight loss.

Язык: Английский

---