Expanding Archaeal Diversity and Phylogeny: Past, Present, and Future

Annual Review of Microbiology, Год журнала: 2021, Номер 75(1), С. 359 - 381

Опубликована: Авг. 5, 2021

The discovery of the Archaea is a major scientific hallmark twentieth century. Since then, important features their cell biology, physiology, ecology, and diversity have been revealed. Over course some 40 years, known archaea has expanded from 2 to about 30 phyla comprising over 20,000 species. Most this archaeal revealed by environmental 16S rRNA gene amplicon sequencing surveys using broad range universal targeted primers. Of few primers that target large fraction diversity, all display bias against recently discovered lineages, which limits studies aiming survey overall diversity. Induced genomic exploration improved phylogenomics approaches, taxonomic classification frequently revised. Due computational limitations continued new stable phylogeny not yet within reach. Obtaining phylogenetic consensus should be high priority for research community.

Язык: Английский

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Vertebrate host phylogeny influences gut archaeal diversity

Nature Microbiology, Год журнала: 2021, Номер 6(11), С. 1443 - 1454

Опубликована: Окт. 26, 2021

Commonly used 16S rRNA gene primers do not detect the full range of archaeal diversity present in vertebrate gut. As a result, several questions regarding component gut microbiota remain, including which Archaea are host-associated, specificities such associations and major factors influencing diversity. Using amplicon sequencing with that specifically target Archaea, we obtained sufficient sequence data from 185 gastrointestinal samples collected 110 species span five taxonomic classes (Mammalia, Aves, Reptilia, Amphibia Actinopterygii), majority were wild. We provide evidence for previously undescribed Archaea-host associations, Bathyarchaeia Methanothermobacter, latter was prevalent among Aves relatively abundant higher body temperatures, although this association could be decoupled host phylogeny. Host phylogeny explained more strongly than diet, while specific taxa associated both factors, cophylogeny significant strongest mammalian herbivores. Methanobacteria only class predicted to last common ancestors mammals all species. Further analysis indicated Archaea-Bacteria interactions have limited effect on These findings expand our current understanding Archaea-vertebrate associations.

Язык: Английский

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Microbiome-immune interactions in tuberculosis

PLoS Pathogens, Год журнала: 2021, Номер 17(4), С. e1009377 - e1009377

Опубликована: Апрель 15, 2021

Tuberculosis (TB) remains an infectious disease of global significance and a leading cause death in low- middle-income countries. Significant effort has been directed towards understanding Mycobacterium tuberculosis genomics, virulence, pathophysiology within the framework Koch postulates. More recently, advent “-omics” approaches broadened our appreciation how “commensal” microbes have coevolved with their host central role shaping health susceptibility to disease. It is now clear that there diverse repertoire interactions between microbiota immune responses can either sustain or disrupt homeostasis. In context efforts combatting TB, such findings knowledge raised important questions: Does microbiome composition indicate determine resistance M . infection? Is development active latent infection upon exposure influenced by microbiome? influence TB therapy outcome risk reinfection ? Can be actively managed reduce recurrence TB? Here, we explore these questions particular focus on microbiome-immune may affect susceptibility, manifestation progression, long-term implications anti-TB therapy, as well potential target for clinical manipulation.

Язык: Английский

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Protozoa populations are ecosystem engineers that shape prokaryotic community structure and function of the rumen microbial ecosystem

The ISME Journal, Год журнала: 2021, Номер 16(4), С. 1187 - 1197

Опубликована: Дек. 9, 2021

Abstract Unicellular eukaryotes are an integral part of many microbial ecosystems where they interact with their surrounding prokaryotic community—either as predators or mutualists. Within the rumen, one most complex host-associated habitats, ciliate protozoa represent main micro-eukaryotes, accounting for up to 50% biomass. Nonetheless, extent ecological effect on community and rumen metabolic output remains largely understudied. To assess role ecosystem, we established in-vitro system in which distinct sub-communities were introduced native community. We show that different communities exert a strong differential impact composition community, well its function including methane production. Furthermore, presence increases diversity specific bacterial populations such Gammaproteobacteria, Prevotella Treponema. Our results suggest contribute maintenance possibly by mitigating competitive exclusion between taxa. findings put forward potentially important ecosystem engineers future microbiome modulation strategies.

Язык: Английский

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Hydrogen and formate production and utilisation in the rumen and the human colon

Animal Microbiome, Год журнала: 2022, Номер 4(1)

Опубликована: Март 14, 2022

Molecular hydrogen (H

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