Genomic analyses of Burkholderia respiratory isolates indicates two evolutionarily distinct B. anthina clades.

Introduction: The Burkholderia cepacia complex (BCC) encompasses a group of at least 22 genetically distinct gram-negatives bacterial species ubiquitous in nature. Recognised as a group of genetically and phenotypically flexible species, the BCC inhabits diverse ecological niches causing both plant and human diseases. Comparative genomic analysis provides an in depth understanding into the population biology, phylogenetic relationship, and genomic architecture of species. Methods: Here, we genomically characterise Burkholderia anthina isolated from patients with chronic lung infections, an understudied pathogen within the Burkholderia cepacia complex. Results: We demonstrate that B. anthina is polyphyletic and constitutes two distinct evolutionary lineages. Core- and pan-genome analyses demonstrated substantial metabolic diversity, with B. anthina Clade I enriched in genes associated with microbial metabolism in diverse environments, including degradation of aromatic compounds and metabolism of xenobiotics, while B. anthina Clade II demonstrated an enhanced capability for siderophore biosynthesis. Discussion: Based on our phylogenetic and comparative genomic analyses, we suggest stratifying B. anthina to recognise a distinct species harbouring increased potential for iron metabolism via siderophore synthesis, for which we propose the name Burkholderia anthinoferum (sp. nov.).

The evolving role of methanogenic archaea in mammalian microbiomes.

Methanogenic archaea (methanogens) represent a diverse group of microorganisms that inhabit various environmental and host-associated microbiomes. These organisms play an essential role in global carbon cycling given their ability to produce methane, a potent greenhouse gas, as a by-product of their energy production. Recent advances in culture-independent and -dependent studies have highlighted an increased prevalence of methanogens in the host-associated microbiome of diverse animal species. Moreover, there is increasing evidence that methanogens, and/or the methane they produce, may play a substantial role in human health and disease. This review addresses the expanding host-range and the emerging view of host-specific adaptations in methanogen biology and ecology, and the implications for host health and disease.

Isolation and characterisation of novel Methanocorpusculum species indicates the genus is ancestrally host-associated.

BACKGROUND: With an increasing interest in the manipulation of methane produced from livestock cultivation, the microbiome of Australian marsupials provides a unique ecological and evolutionary comparison with 'low-methane' emitters. Previously, marsupial species were shown to be enriched for novel lineages of Methanocorpusculum, as well as Methanobrevibacter, Methanosphaera, and Methanomassiliicoccales. Despite sporadic reports of Methanocorpusculum from stool samples of various animal species, there remains little information on the impacts of these methanogens on their hosts. RESULTS: Here, we characterise novel host-associated species of Methanocorpusculum, to explore unique host-specific genetic factors and their associated metabolic potential. We performed comparative analyses on 176 Methanocorpusculum genomes comprising 130 metagenome-assembled genomes (MAGs) recovered from 20 public animal metagenome datasets and 35 other publicly available Methanocorpusculum MAGs and isolate genomes of host-associated and environmental origin. Nine MAGs were also produced from faecal metagenomes of the common wombat (Vombatus ursinus) and mahogany glider (Petaurus gracilis), along with the cultivation of one axenic isolate from each respective animal; M. vombati (sp. nov.) and M. petauri (sp. nov.). CONCLUSIONS: Through our analyses, we substantially expand the available genetic information for this genus by describing the phenotypic and genetic characteristics of 23 host-associated species of Methanocorpusculum. These lineages display differential enrichment of genes associated with methanogenesis, amino acid biosynthesis, transport system proteins, phosphonate metabolism, and carbohydrate-active enzymes. These results provide insights into the differential genetic and functional adaptations of these novel host-associated species of Methanocorpusculum and suggest that this genus is ancestrally host-associated.

Culture- and metagenomics-enabled analyses of the Methanosphaera genus reveals their monophyletic origin and differentiation according to genome size.

The genus Methanosphaera is a well-recognized but poorly characterized member of the mammalian gut microbiome, and distinctive from Methanobrevibacter smithii for its ability to induce a pro-inflammatory response in humans. Here we have used a combination of culture- and metagenomics-based approaches to expand the representation and information for the genus, which has supported the examination of their phylogeny and physiological capacity. Novel isolates of the genus Methanosphaera were recovered from bovine rumen digesta and human stool, with the bovine isolate remarkable for its large genome size relative to other Methanosphaera isolates from monogastric hosts. To substantiate this observation, we then recovered seven high-quality Methanosphaera-affiliated population genomes from ruminant and human gut metagenomic datasets. Our analyses confirm a monophyletic origin of Methanosphaera spp. and that the colonization of monogastric and ruminant hosts favors representatives of the genus with different genome sizes, reflecting differences in the genome content needed to persist in these different habitats.