Rarefaction is currently the best approach to control for uneven sequencing effort in amplicon sequence analyses

mSphere, Journal Year: 2024, Volume and Issue: 9(2)

Published: Jan. 22, 2024

ABSTRACT Considering it is common to find as much 100-fold variation in the number of 16S rRNA gene sequences across samples a study, researchers need control for effect uneven sequencing effort. How do this has become contentious question. Some have argued that rarefying or rarefaction “inadmissible” because omits valid data. A alternative approaches been developed normalize and rescale data purport be invariant observations. I generated community distributions based on 12 published sets where was able assess ability multiple methods Rarefaction only method could effort when measuring commonly used alpha beta diversity metrics. Next, compared false detection rate power detect true differences between simulated communities with known size using various Although all controlling had an acceptable were randomly assigned two treatment groups, consistently depth confounded group. Finally, statistical metrics highest rarefaction. These simulations underscore importance amplicon analyses. IMPORTANCE Sequencing fragments fundamental tool understanding microbial factors affect their diversity. Due technical challenges, observe wide are collected from different within same study. However, by ecologists sensitive Therefore, tools needed levels sequencing. This simulation-based analysis shows despite longstanding controversy, most robust approach The controversy started confusion over definition violation assumptions made borrowed other fields. Microbial should use

Language: Английский

---

The role of animal hosts in shaping gut microbiome variation

Philosophical Transactions of the Royal Society B Biological Sciences, Journal Year: 2024, Volume and Issue: 379(1901)

Published: March 18, 2024

Millions of years co-evolution between animals and their associated microbial communities have shaped diversified the nature relationship. Studies continue to reveal new layers complexity in host–microbe interactions, fate which depends on a variety different factors, ranging from neutral processes environmental factors local dynamics. Research is increasingly integrating ecosystem-based approaches, metagenomics mathematical modelling disentangle individual contribution ecological microbiome evolution. Within this framework, host are known be among dominant drivers composition animal species. However, extent they shape assembly evolution remains unclear. In review, we summarize our understanding how drive these dynamics conserved vary across taxa. We conclude by outlining key avenues for research highlight need implementation modifications existing theory fully capture host-associated microbiomes. This article part theme issue ‘Sculpting microbiome: determine respond colonization’.

Language: Английский

---

Contamination source modeling with SCRuB improves cancer phenotype prediction from microbiome data

Nature Biotechnology, Journal Year: 2023, Volume and Issue: 41(12), P. 1820 - 1828

Published: March 16, 2023

Language: Английский

---

Host species and habitat shape fish-associated bacterial communities: phylosymbiosis between fish and their microbiome

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

Published: Nov. 20, 2023

While many studies have reported that the structure of gut and skin microbiota is driven by both species-specific habitat-specific factors, relative importance host-specific versus environmental factors in wild vertebrates remains poorly understood. The aim this study was to determine diversity composition fish skin, gut, surrounding water bacterial communities (hereafter referred as microbiota) assess extent which host habitat phylogeny predict similarity. Skin swabs samples from 334 belonging 17 species were sampled three Laurentian Great Lakes (LGLs) habitats (Detroit River, Lake Erie, Ontario). We also collected filtered at time collection. analyzed community using 16S metabarcoding tested for variation.We found distinct microbiota, although more closely resembled microbiota. (sample location), habitat, diet, shape promote divergence or convergence Since significantly affected (separately effects), we phylosymbiosis pairwise phylogenetic distance dissimilarity. significant effects on dissimilarity, consistent with perhaps reflecting longstanding co-evolutionary relationship between their microbiomes.Analyzing mucus across diverse complex natural ecosystems such LGLs provides insights into potential microbiome, ultimately health, host. Video Abstract.

Language: Английский

---

The intestinal digesta microbiota of tropical marine fish is largely uncultured and distinct from surrounding water microbiota

npj Biofilms and Microbiomes, Journal Year: 2024, Volume and Issue: 10(1)

Published: Feb. 19, 2024

Studying the gut microbes of marine fishes is an important part conservation as many fish species are increasingly threatened by extinction. The microbiota only a small fraction more than 32,000 known has been investigated. In this study we analysed intestinal digesta composition 50 different wild from tropical waters. Our results show that harbour distinct surrounding water and location, domestication status, host intrinsic factors strongly associated with composition. Furthermore, vast majority (~97%) fish-associated microorganisms do not have any cultured representative. Considering impact on health physiology, these findings underpin call to also preserve species, especially those may be exposed habitat destruction.

Language: Английский

---

Spatial and temporal changes in gut microbiota composition of farmed Asian seabass ( Lates calcarifer ) in different aquaculture settings

Microbiology Spectrum, Journal Year: 2025, Volume and Issue: unknown

Published: March 14, 2025

ABSTRACT The microbiota composition of healthy farmed fishes remains poorly characterized for many species. This study explores the influence external environment and innate factors that may shape gut Asian seabass, Lates calcarifer . α-diversity based on Shannon, Simpson, Chao1 indices was lower reared in sea cages tanks than experienced a transfer from to tanks. Longitudinal analyses segments revealed no significant differences alpha diversity between within same containment type, except index stomach pyloric cecum sea-caged fishes. β-diversity analysis using weighted UniFrac distance Bray-Curtis dissimilarity demonstrated fish type shared similar microbial communities. PERMANOVA tests confirmed farm, batch significantly influenced these distances. Containment accounted 10.4% observed diversity, farm 29.8%, 10.7%. Genera comprising potential pathogens such as Aeromonas , Flavobacterium Vibrio were differentially abundant along guts different types particularly increased Microbiota changes with host age segment, genera identified seabass grew. Comparing hindgut other species host-specific clustering indicated by PERMANOVA. Overall, findings underscore significance conditions broad implications aquaculture practices. IMPORTANCE Understanding is crucial optimizing highlights ( ). By demonstrating community are shaped location, batch, research provides valuable insights into how environmental interact health. findings, differential abundance various types, need tailored management strategies aquaculture. not only advances our knowledge but also has improving sustainability productivity

Language: Английский

---

Important role of endogenous microbial symbionts of fish gills in the challenging but highly biodiverse Amazonian blackwaters

Nature Communications, Journal Year: 2023, Volume and Issue: 14(1)

Published: July 6, 2023

Abstract Amazonian blackwaters are extremely biodiverse systems containing some of Earth’s most naturally acidic, dissolved organic carbon -rich and ion‐poor waters. Physiological adaptations fish facing these ionoregulatory challenges unresolved but could involve microbially-mediated processes. Here, we characterize the physiological response 964 fish-microbe from four blackwater Teleost species along a natural hydrochemical gradient, using dual RNA-Seq 16 S rRNA gill samples. We find that host transcriptional responses to species-specific, occasionally include overexpression Toll-receptors integrins associated interkingdom communication. Blackwater microbiomes characterized by transcriptionally-active betaproteobacterial cluster potentially interfering with epithelial permeability. explore further interactions analyzing transcriptomes axenic zebrafish larvae exposed sterile, non-sterile inverted (non-native bacterioplankton) blackwater. survive poorly when sterile/inverted Overall, our results suggest critical role for endogenous symbionts in physiology.

Language: Английский

---

Microbial diversity in mountain-dwelling amphibians: The combined effects of host and climatic factors

iScience, Journal Year: 2024, Volume and Issue: 27(6), P. 109907 - 109907

Published: May 3, 2024

Comprehending the determinants of host-associated microbiota is pivotal in microbial ecology. Yet, links between climatic factors and variations necessitate further clarification. Mountain-dwelling amphibians, with limited dispersal abilities, serve as valuable models for addressing these questions. Our study, using 126 amphibian-associated samples (64 gut 62 skin) 101 environmental (51 soil 50 water) from eastern Tibetan Plateau, revealed host primary drivers microbiota. However, contributed to additional beta-diversity skin function. Water were identified a significant contributor microbiomes, their climate-driven mediating an indirect association These findings extend our understanding assembly emphasizing significance evaluating impact climate change on animals.

Language: Английский

---

A new and widespread group of fish apicomplexan parasites

Current Biology, Journal Year: 2024, Volume and Issue: 34(12), P. 2748 - 2755.e3

Published: May 30, 2024

Language: Английский

---

Regulation of host gene expression by gastrointestinal tract microbiota in Chinook Salmon (Oncorhynchus tshawytscha)

Molecular Ecology, Journal Year: 2023, Volume and Issue: 32(15), P. 4427 - 4446

Published: June 7, 2023

Abstract Differences in gut microbiome composition are linked with health, disease and ultimately host fitness; however, the molecular mechanisms underlying that relationship not well characterized. Here, we modified fish microbiota using antibiotic probiotic feed treatments to address effect of on gene expression patterns. Chinook salmon ( Oncorhynchus tshawytscha ) was evaluated whole transcriptome sequencing (RNA‐Seq) hindgut mucosa samples from individuals treated antibiotic, control diets determine differentially expressed (DE) genes. Fifty DE genes were selected for further characterization nanofluidic qPCR chips. We used 16S rRNA metabarcoding characterize rearing water (bacterial) communities. Daily administration antibiotics probiotics resulted significant changes aquatic as more than 100 treatment fish, relative healthy controls. Normal depletion by mostly led downregulation different aspects immunity upregulation apoptotic process. In treatment, related post‐translation modification inflammatory responses up‐regulated Our results revealed effects (antibiotic probiotic) rabep2, aifm3, manf, prmt3 transcription. Moreover, found associations between members Lactobacillaceae Bifidobacteriaceae Overall, our analysis showed had impacts many signalling pathways, specifically targeting immune, developmental metabolic processes. some involved microbiome‐host interactions will help develop new strategies preventing/ treating disruption‐related diseases.

Language: Английский

---