A global genomic atlas of >7,000 MAGs/genomes from infants, domesticated animals, non-human primates, and ancient humans helps explain subspecies differentiation in the gut microbiota of Western and non-Western infants and provides a framework for community-mediated interventions in early life.
Megasphaera elsdenii is best known as a prominent lactate consumer within the rumen microbial community in livestock, and its metabolic properties are relatively well studied. In humans, it can be isolated from healthy donors’ feces and, more often, from patients’ feces with diverse inflammatory conditions. Genetic diversity of this species is poorly understood, and it is currently unclear whether human and animal gut isolates are genetically related and perform the same metabolic function. In this study, we compared 86 M. elsdenii genomes from human feces (as a proxy for the human gut) to those of animal gut isolates. Phylogenetic analysis revealed that human and animal gut lineages intermingle within a single, genetically homogeneous branch, lacking any host-specific clustering. Human gut lineages shared most of their genes and biochemical pathways with those of swine and cattle gut isolates, despite differences in their digestive tracts. Neither unsupervised nor supervised approaches identified any notable differences in encoded pathways between different host-specific gut lineages. Genome-scale metabolic modeling suggests that human and animal gut lineages likely share identical carbon and energy source requirements. Moreover, the requirements for lactate and acetate were conserved across all studied samples, regardless of the host. Finally, we found no virulence genes, and lactate utilization remains a plausible explanation for M. elsdenii accumulation in the host intestine. IMPORTANCE Megasphaera elsdenii is considered a commensal in the human gut and animal rumen. However, M. elsdenii tends to be more abundant in patients’ feces with diverse inflammatory conditions. As we know little about the strain diversity and biology of human gut lineages, comparisons with better-studied animal isolates can be informative. In this study, we compared human gut M. elsdenii genomes to those from better-studied isolates from ruminant and non-ruminant animal hosts. Human gut samples associated with patients and healthy donors were genetically very similar to gut isolates from animals and may have shared a common origin. We found that human and animal gut lineages have a similar genomic makeup and metabolic potential, and that neither group harbors virulence genes. We hypothesize that M. elsdenii is a benign commensal that grows in response to lactate accumulation in the inflamed gut.
D. Sabirova, M. Rayko, V.B. Vinichenko et al.· bioRxiv· 0 citations
This study reconstructed the first comprehensive pangenome of B. bifidum using 1,351 high-quality genomes, including metagenome-assembled genomes to identify species-specific genetic and functional features and identified significant gain-of-function events.
Emanuele Selleri, G. Longhi, C. Tarracchini et al.· Microbiome Research Reports· 0 citations
This study provides genome- and spatially resolved views of dominant SCB in holothurians and offers evolutionary insights into host-interface diversification in the deep-sea holothurian body wall.
The semi-domesticated gayal (Bos frontalis) is an endangered browsing ruminant inhabiting the rugged Eastern Himalayan foothills, and maintains an energy-intensive lifestyle on nutrient-poor, fiber-rich feed. However, the dietary, microbial, and host physiological features underlying this adaptation remain poorly understood. Here, we analyzed fecal metagenomes from ten bovine populations (n = 334) to characterize dietary composition. Then we profiled the four-chambered (FC) stomach microbiome in adult gayal (Bos frontalis), yak (Bos grunniens), and taurine cattle (Bos taurus). Host transcriptomes were profiled across the FC stomach in adult individuals from gayal, yak and cattle. Dietary analysis revealed a woody plant-dominated, bamboo-rich dietary pattern in gayal. Gastric metagenomes in gayal showed high population-level microbial diversity, pronounced individual-associated community structure, and functional potentials related to aromatic compound transformation, nitrogen metabolism, and metabolic flexibility. Transcriptomes revealed compartment-specific specialization in the gayal stomach, including rumen immune signatures and reticulum contractile/electrophysiological features. Exploratory compartment-level integration further suggested possible consistency between host transcriptomic features and microbial functional potential. Together, these multi-omics findings suggest a host-microbiome system potentially associated with the utilization of chemically complex, low-quality forage, providing a framework for understanding digestive features of browsing ruminants and for conserving host-associated gastrointestinal microbiomes.
Yuming Chen, Juntao Ma, Zhifan Guo et al.· npj Biofilms and Microbiomes· 1 citation
This study demonstrates that several Bifidobacterium species residing in the gut of gummivorous primates, such as marmosets, possess previously uncharacterised pathways for the efficient utilisation of type-II arabinogalactan (AG), the major polysaccharide component of tree gums.
Yuki Sasaki, Tomoya Kozakai, Moe Inoue et al.· The ISME Journal· 0 citations
The tropical forests of Mesoamerica, stretching from Mexico to northern Colombia, represent one of the most diverse biotas on Earth. Yet their evolutionary history and the processes that shape their assembly remain poorly understood, often leading to their treatment as a single biotic unit. In this study, we use the family Annonaceae as a model lineage to reconstruct the region’s evolutionary trajectories, integrating hundreds of nuclear markers derived from both historical and contemporary herbarium specimens. This high-resolution phylogenomic framework, encompassing more than 80 % of the ~2,500 species in the family, reveals consistent patterns of floristic and evolutionary differentiation, as well as sharp contrasts between northern Mesoamerica (MegaMexico 2 and the Caribbean) and the southern regions. Northern areas exhibit deeper phylogenetic diversity despite lower species richness, reflecting prolonged isolation and greater environmental heterogeneity. In contrast, the south shows high species richness but phylogenetic redundancy, driven by recent colonizations and climatic filters. Divergence times highlight the central role of Miocene-Pliocene climatic oscillations and more recent orogenic activity in shaping Mesoamerican forests: dry forests emerge as evolutionary refugia and center of radiation. In contrast, wet forests consistently harbor younger lineages. Taken together, these findings challenge the view of Mesoamerica as a single evolutionary unit and demonstrate that its tropical forests are dynamic systems, repeatedly molded by cycles of climatic change and geographic isolation.
Andrés Ernesto Ortíz Rodríguez, Laura Holzmeyer, Leopoldo Hurtado-Reveles et al.· Botanical Sciences· 1 citation
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