Novel lineages of bacteria with reduced genomes from the gut of farm animals.
Abstract: Genome reduction and associated metabolic deficiencies have been described in various lineages of parasitic and symbiotic microorganisms that obtain essential nutrients from their partners, and in some free-living microorganisms that inhabit stable environments. The animal gut is a relatively stable ecosystem, characterized by an abundance of organic substances and a high concentration of microorganisms, which provides favorable conditions for the survival of microorganisms with reduced genomes. Metagenomic analysis of 49 samples of feces of farm animals (cows, sheep, yaks, and horses) revealed uncultured lineages of bacteria with reduced genomes (<1 Mbp): family UBA1242 (, ), order Rs-D84 (), and family UBA9783 (, ), defined in genome-taxonomy database. Analysis of the genomes showed that these bacteria lacked pathways for the biosynthesis of amino acids, nucleotides, lipids, and many other essential metabolites. The UBA9783 genomes encoded a near-complete Embden-Meyerhof glycolytic pathway and the non-oxidative phase of the pentose phosphate pathway, while in UBA1242 and Rs-D84, these pathways are incomplete. All bacteria are limited to fermentative metabolism and lack aerobic and anaerobic respiratory pathways. All UBA9783 and some Rs-D84 genomes encoded FF-type ATP synthase and pyrophosphate-energized proton pump; they also can import and utilize peptides and some amino acids. While UBA9783 bacteria could thrive as specialized free-living organisms in the organic-rich gut environment, the UBA1242 and Rs-D84 lineages appear to have adopted the lifestyle of an obligate symbiont/parasite, obtaining metabolites from other cells.IMPORTANCEThe microbiota of the animal gastrointestinal tracts is a complex community of microorganisms which interact in a synergistic or antagonistic relationship and play key nutritional and metabolic roles. However, despite its importance, the gut microbiota of farm animals, especially its uncultured majority, remains largely unexplored. We performed a metagenomic analysis of the gut microbiome of farm animals and characterized three uncultured lineages of bacteria with reduced genomes (<1 Mbp) from the phyla , , and . These bacteria were predicted to possess key metabolic deficiencies such as the inability to synthesize essential cell metabolites, suggesting their adaptation to the lifestyle of a symbiont/parasite, or a scavenger obtaining nutrients from the organic-rich gut environment. This study shows that genome reduction with metabolic specialization and adaptation to a partner-dependent lifestyle occurred through convergent evolution in several phylogenetically distant lineages of gut microbiota.
Publication Date: 2025-06-30 PubMed ID: 40586543PubMed Central: PMC12306168DOI: 10.1128/msphere.00294-25Google Scholar: Lookup
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Summary
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This research outlines the discovery of new strains of bacteria with smaller genomes than usual, located in the gut of farm animals. This was discovered through a detailed analysis of the fecal samples. The bacteria seem to survive by obtaining essential nutrients in a symbiotic/parasitic manner from their environment or by scavenging for nutrients.
About The Research
- The research involved a metagenomic evaluation of 49 farm animal samples, specifically, fecal matter from cows, sheep, yaks, and horses.
- Upon analysis, unique strains of bacteria that possess remarkably reduced genomes were discovered, i.e., less than 1Mbp. These strains are dubbed family UBA1242, order Rs-D84, and family UBA9783 as defined by the genome-taxonomy database.
In-Depth Findings
- The specific genomes of these types of bacteria show that they don’t have the necessary processes to synthesize significant metabolites including amino acids, nucleotides and lipids.
- Although there were variances in their metabolic pathways, it was common for these bacteria to lack aerobic and anaerobic respiratory pathways, leading to a reliance on fermentative metabolism.
- Specifically, UBA9783 bacteria had capabilities in the near-complete Embden-Meyerhof glycolytic route and non-oxidative phases of pentose phosphate pathways. This is in contrast to UBA1242 and Rs-D84 where these pathways are incomplete.
Methodologies Of Survival
- Some of these bacterial strains, like Rs-D84 and UBA9783, had genomes that harbored the FF-type ATP synthase and pyrophosphate-energized proton pump, which allowed them to import and utilize peptides and some amino acids.
- There’s a suggestion of these types of bacteria being equipped to thrive as specialized free-living organisms in environments rich with organic matter, like the gut infrastructures of farm animals. Particularly, UBA9783 bacteria appear to be adapted to survive as scavengers in the organic-rich gut environment.
- On the other hand, the UBA1242 and Rs-D84 lineages seem to have adopted a more symbiotic/parasitic lifestyle, obtaining essential metabolites directly from other cells.
Importance Of The Findings
- The gut microbiome of farm animals plays an integral role nutritionally and metabolically, consisting of a symbiotic and antagonistic relationship of complex microorganism communities. Nonetheless, there remains a significant gap in understanding of this microbiota, notably so for its uncultivable majority.
- This research deepened our understanding of these uncultivated bacteria lineages with uniquely reduced genomes, breaking new ground into the investigation of gut microbiota.
- This suggests the phenomena of genome size reduction, metabolic specialization, and lifestyle adaptation occurring through convergent evolution in gut microbiota across different lineages. This adaptive approach appears to be common in the farm animal gut environment rotating around specific nutrition acquisition strategies.
Cite This Article
APA
Begmatov S, Beletsky AV, Mardanov AV, Lukina AP, Glukhova LB, Karnachuk OV, Ravin NV.
(2025).
Novel lineages of bacteria with reduced genomes from the gut of farm animals.
mSphere, 10(7), e0029425.
https://doi.org/10.1128/msphere.00294-25 Publication
Researcher Affiliations
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia.
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia.
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia.
- Tomsk State University, Tomsk, Russia.
- Tomsk State University, Tomsk, Russia.
- Tomsk State University, Tomsk, Russia.
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia.
MeSH Terms
- Animals
- Genome, Bacterial
- Gastrointestinal Microbiome / genetics
- Bacteria / genetics
- Bacteria / classification
- Bacteria / isolation & purification
- Feces / microbiology
- Phylogeny
- Animals, Domestic / microbiology
- Metagenomics
- Cattle
- Sheep
- Horses / microbiology
Grant Funding
- Ministry of Science and Higher Education of the Russian Federation (Minobrnauki of Russia)
Conflict of Interest Statement
The authors declare no conflict of interest.
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