Culture‐Independent Species‐Level Taxonomic and Functional Characterisation of Bacteroides, the Core Bacterial Genus Within Reptile Guts

Molecular Ecology, Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 7, 2025

The genus Bacteroides is a widespread and abundant bacterial taxon associated with gut microbiotas. Species within fill many niches, including as mutualists, commensals pathogens for their hosts. Within reptiles, dominant, 'core' bacterium that sometimes exhibits increased abundance in times of food scarcity, such during hibernation. Here, we take two-pronged approach to better characterise populations reptile guts. Firstly, leverage published 16S rRNA gene sequence datasets determine the species-level distributions members Secondly, mine publicly available metagenomes extract data from birds, amphibians mammals, compare functional potential different host taxa. analyses revealed B. acidifaciens most common species guts, orders reptiles differ which they harbour. taxonomy recovered metagenomic assembly did not between or substantially across mammals. Metagenome-assembled genomes were marginally more related when hosts closely related, particular harbouring markedly unique MAGs compared other Our findings indicate harbour similar profiles broad comparisons, but some differences groups, appears perform largely roles vertebrate guts regardless relatedness.

Language: Английский

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Gut microbiome of the sole surviving member of reptile order Rhynchocephalia reveals biogeographic variation, influence of host body condition and a substantial core microbiota in tuatara across New Zealand

Ecology and Evolution, Journal Year: 2024, Volume and Issue: 14(2)

Published: Feb. 1, 2024

Tuatara are the sole extant species in reptile order Rhynchocephalia. They ecologically and evolutionarily unique, having been isolated geographically for ~84 million years from their closest living relatives ~250 years. Here we report tuatara gut bacterial community first time. We sampled microbiota of translocated at five sanctuaries spanning a latitudinal range ~1000 km within Aotearoa New Zealand, as well individuals source population on Takapourewa (Stephens Island). This represents look Rhynchocephalia provides opportunity to address several key hypotheses, namely that microbiota: (1) differs those other orders; (2) varies among geographic locations but is more similar sites with temperatures (3) shaped by body condition, parasitism ambient temperature. found significant drivers sampling site, temperature, suggesting importance these factors when considering conservation. also derived 'core' shared bacteria across many sites, despite isolation. Remarkably, >70% amplicon sequence variants could not be assigned known genera, largely undescribed this ancient host species.

Language: Английский

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Season, Body Condition and Developmental Stage Influence the Gut Microbiota of the Sole Living Rhynchocephalian Reptile (Sphenodon punctatus)

Ecology and Evolution, Journal Year: 2025, Volume and Issue: 15(4)

Published: April 1, 2025

Seasonality plays a crucial role for many species, especially reptiles. In multiple reptile seasonality has been linked to shifts in the gut microbiota, influenced by factors, such as ambient temperature, food availability and shifting host function across different seasons. We tested whether tuatara, an endemic New Zealand sole extant member of order Rhynchocephalia, maintains stable microbiota over 2 years sampling three seasons (summer, autumn, spring) or if dominant bacterial community varies with season. found that diversity changed significantly seasonally, most diverse spring. also season beta-diversity, did tuatara developmental stage, body condition tick abundance. However, there was little evidence recurring seasonal assemblage 2024 compared 2023. For where same individual resampled seasons, composition appeared be correlated time sampling, closer temporal samples more similar one another than taken further apart, which seen significance period factor explaining variation all tuatara. identified genera increased decreased each Despite notable among particularly exhibits remarkable persistence time, including within individuals.

Language: Английский

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Limited gut bacterial response of tuatara (Sphenodon punctatus) to dietary manipulation and captivity

FEMS Microbiology Ecology, Journal Year: 2024, Volume and Issue: 100(11)

Published: Oct. 14, 2024

The bacteria of a host's digestive tract play crucial roles in digestion and pathogen resistance. Hosts living captivity often have more human interaction antibiotic use, addition to differences diet environment, compared their wild counterparts. Consequently, captive animals frequently harbour different bacterial communities. We tested whether diversity provided shifts the gut tuatara, an endemic New Zealand reptile, at three sites, examined how community these tuatara compares those wild. Dietary manipulation did not cause strong overall shift bacteria, but individual experience during manipulation, which subsequently reverted after manipulation. found that Bacteroides, genus common most vertebrate guts rare increased significantly then decreased post-manipulation. Finally, differed from though dominant genera persisted tuatara. This work represents first investigation establishes sensitivity dietary for this relict reptile.

Language: Английский

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Absolute abundance unveilsBasidiobolusas a cross-domain bridge indirectly bolstering gut microbiome homeostasis

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Dec. 28, 2024

Abstract The host microbiome is integral to metabolism, immune function, and resilience against pathogens. However, reliance on relative abundance (RA) estimate host-associated microbiomes introduces compositional biases, while limited tools for absolute (AA) quantification hinder broader applications. To address these challenges, we developed DspikeIn ( https://github.com/mghotbi/DspikeIn ), an R package paired with a versatile wet-lab methodology AA quantification. Using RA compare core distributions across herpetofauna orders their natural histories revealed starkly distinct results, driven by aggregate effects, including inherited biases in additional multifactorial influences. Focusing two closely related Desmognathus species demonstrated that enhanced resolution differential analyses minimized false discovery rates (FDR) when identifying enriched taxa gut microbiomes. Keystone identified through network associations also differed between data. For example, Lactococcus Cetobacterium were members Anura Caudata, Basidiobolus Mortierella Chelonia Squamata, facilitating adaptation diverse environments, insights undetectable AA-based analysis further removing the subnetwork increased negative interactions, highlighting its role promoting homeostasis cross-domain connectivity. Despite low redundancy, node exhibited high betweenness, efficiency, degree, serving as critical bridge linking disconnected nodes or modules indirectly supporting stability, consistent Burt’s structural hole theory. represents transformative tool research, enabling transition from delivering more accurate, consistent, comparable results studies. Graphical abstract cheatsheet

Language: Английский

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