Microbiome differential abundance methods produce different results across 38 datasets

Nature Communications, Journal Year: 2022, Volume and Issue: 13(1)

Published: Jan. 17, 2022

Identifying differentially abundant microbes is a common goal of microbiome studies. Multiple methods are used interchangeably for this purpose in the literature. Yet, there few large-scale studies systematically exploring appropriateness using these tools interchangeably, and scale significance differences between them. Here, we compare performance 14 differential abundance testing on 38 16S rRNA gene datasets with two sample groups. We test amplicon sequence variants operational taxonomic units (ASVs) Our findings confirm that identified drastically different numbers sets significant ASVs, results depend data pre-processing. For many number features correlate aspects data, such as size, sequencing depth, effect size community differences. ALDEx2 ANCOM-II produce most consistent across agree best intersect from approaches. Nevertheless, recommend researchers should use consensus approach based multiple to help ensure robust biological interpretations. Many available, but it lacks systematic comparison among authors groups, show results.

Language: Английский

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Microbiota–gut–brain axis and its therapeutic applications in neurodegenerative diseases

Signal Transduction and Targeted Therapy, Journal Year: 2024, Volume and Issue: 9(1)

Published: Feb. 16, 2024

Abstract The human gastrointestinal tract is populated with a diverse microbial community. vast genetic and metabolic potential of the gut microbiome underpins its ubiquity in nearly every aspect biology, including health maintenance, development, aging, disease. advent new sequencing technologies culture-independent methods has allowed researchers to move beyond correlative studies toward mechanistic explorations shed light on microbiome–host interactions. Evidence unveiled bidirectional communication between central nervous system, referred as “microbiota–gut–brain axis”. microbiota–gut–brain axis represents an important regulator glial functions, making it actionable target ameliorate development progression neurodegenerative diseases. In this review, we discuss mechanisms As provides essential cues microglia, astrocytes, oligodendrocytes, examine communications microbiota these cells during healthy states Subsequently, diseases using metabolite-centric approach, while also examining role microbiota-related neurotransmitters hormones. Next, targeting intestinal barrier, blood–brain meninges, peripheral immune system counteract dysfunction neurodegeneration. Finally, conclude by assessing pre-clinical clinical evidence probiotics, prebiotics, fecal transplantation A thorough comprehension will foster effective therapeutic interventions for management

Language: Английский

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The gut microbiome and hypertension

Nature Reviews Nephrology, Journal Year: 2023, Volume and Issue: 19(3), P. 153 - 167

Published: Jan. 11, 2023

Language: Английский

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Quantifying bias introduced by sample collection in relative and absolute microbiome measurements

Nature Biotechnology, Journal Year: 2023, Volume and Issue: 42(2), P. 328 - 338

Published: April 27, 2023

Language: Английский

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Gut microbiota in overweight and obesity: crosstalk with adipose tissue

Nature Reviews Gastroenterology & Hepatology, Journal Year: 2023, Volume and Issue: 21(3), P. 164 - 183

Published: Dec. 8, 2023

Language: Английский

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The overlooked evolutionary dynamics of 16S rRNA revises its role as the “gold standard” for bacterial species identification

Scientific Reports, Journal Year: 2024, Volume and Issue: 14(1)

Published: April 20, 2024

Abstract The role of 16S rRNA has been and largely remains crucial for the identification microbial organisms. Although could certainly be described as one most studied sequences ever, current view it somewhat ambiguous. While some consider to a variable marker with resolution power down strain level, others them living fossils that carry information about origin domains cellular life. We show is clearly an evolutionarily very rigid sequence, making unique irreplaceable marker, but its applicability beyond genus level highly limited. Interestingly, seems evolutionary rigidity not driven by functional constraints sequence (RNA–protein interactions), rather results from characteristics host organism. Our suggest that, at least in lineages, Horizontal Gene Transfer (HGT) within genera plays important non-dynamics (stasis) rRNA. Such exhibit apparent lack diversification comparison rest genome. However, why limited specifically solely enigmatic.

Language: Английский

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A comprehensive overview of microbiome data in the light of machine learning applications: categorization, accessibility, and future directions

Frontiers in Microbiology, Journal Year: 2024, Volume and Issue: 15

Published: Feb. 13, 2024

Metagenomics, Metabolomics, and Metaproteomics have significantly advanced our knowledge of microbial communities by providing culture-independent insights into their composition functional potential. However, a critical challenge in this field is the lack standard comprehensive metadata associated with raw data, hindering ability to perform robust data stratifications consider confounding factors. In review, we categorize publicly available microbiome five types: shotgun sequencing, amplicon metatranscriptomic, metabolomic, metaproteomic data. We explore importance for reuse address challenges collecting standardized metadata. also, assess limitations collection existing public repositories metagenomic This review emphasizes vital role interpreting comparing datasets highlights need protocols fully leverage data's Furthermore, future directions implementation Machine Learning (ML) retrieval, offering promising avenues deeper understanding ecological roles. Leveraging these tools will enhance capabilities dynamics diverse ecosystems. Finally, emphasize crucial ML models development.

Language: Английский

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De-biasing microbiome sequencing data: bacterial morphology-based correction of extraction bias and correlates of chimera formation

Microbiome, Journal Year: 2025, Volume and Issue: 13(1)

Published: Feb. 4, 2025

Abstract Introduction Microbiome amplicon sequencing data are distorted by multiple protocol-dependent biases from bacterial DNA extraction, contamination, sequence errors, and chimeras, hindering clinical microbiome applications. In particular, extraction bias is a major confounder in sequencing-based analyses, with no correction method available to date. Here, we suggest using mock community controls computationally correct based on morphological properties. Methods We compared dilution series of 3 cell communities an even or staggered composition. these mock, additional skin samples, was extracted 8 different protocols (2 buffers, 2 kits, lysis conditions). Extracted sequenced (V1–V3 16S rRNA gene) together corresponding mocks. Results composition significantly between kits conditions, but not buffers. Independent the protocol, chimera formation increased higher input numbers. Contaminants originated mostly considerable cross-contamination observed low-input samples. Comparing mocks revealed taxon-specific bias. Strikingly, this per species predictable morphology. Morphology-based computational improved resulting microbial compositions when applied taxa. Equivalent samples showed substantial impact compositions. Conclusions Our results indicate that density increases during PCR amplification. Furthermore, show morphology would be feasible appropriate positive controls, thus constituting important step toward overcoming protocol analysis.

Language: Английский

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Benchmarking short-read metagenomics tools for removing host contamination

GigaScience, Journal Year: 2025, Volume and Issue: 14

Published: Jan. 1, 2025

The rapid evolution of metagenomic sequencing technology offers remarkable opportunities to explore the intricate roles microbiome in host health and disease, as well uncover unknown structure functions microbial communities. However, swift accumulation data poses substantial challenges for analysis. Contamination from DNA can substantially compromise result accuracy increase additional computational resources by including nontarget sequences. In this study, we assessed impact decontamination on downstream analyses, highlighting its importance producing accurate results efficiently. We also evaluated performance conventional tools like KneadData, Bowtie2, BWA, KMCP, Kraken2, KrakenUniq, each offering unique advantages different applications. Furthermore, highlighted an reference genome, noting that absence negatively affected across all tools. Our findings underscore need careful selection genomes enhance analyses. These insights provide valuable guidance improving reliability reproducibility research.

Language: Английский

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Resistome expansion in disease-associated human gut microbiomes

Microbiome, Journal Year: 2023, Volume and Issue: 11(1)

Published: July 29, 2023

Abstract Background The resistome, the collection of antibiotic resistance genes (ARGs) in a microbiome, is increasingly recognised as relevant to development clinically resistance. Many metagenomic studies have reported resistome differences between groups, often connection with disease and/or treatment. However, consistency associations antibiotic- and non-antibiotic–treated diseases has not been established. In this study, we re-analysed human gut microbiome data from 26 case-control assess link resistome. Results highly variable individuals both within studies, but may also vary significantly case control groups even absence large taxonomic differences. We found that for commonly treated antibiotics, namely cystic fibrosis diarrhoea, patient microbiomes had elevated ARG abundances compared controls. Disease-associated expansion was when abundance high controls, suggesting ongoing additive acquisition disease-associated strains. trend increased cases some on are such colorectal cancer. Conclusions Diseases antibiotics associated expanded resistomes, historical exposure exerted considerable selective pressure

Language: Английский

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