Genomic Analyses of Bifidobacterium moukalabense Reveal Adaptations to Frugivore/Folivore Feeding Behavior

Funding: This research was funded by the Japan Science and Technology Agency (JST) and Japan International Cooperation Agency (JICA), grant for the Science and Technology Research Partnership for Sustainable Development (SATREPS) “Conservation of Biodiversity in Tropical Forest through Sustainable Coexistence between Human and Wild Animals” (PI, Juichi Yamagiwa) and the study was also supported by Grants-in-Aid for Scientific Research (15K18775, Sayaka Tsuchida)”. Acknowledgments: We thank Ayumi Akiyoshi and Chiaki Hagiwara for technical assistance and Takahiro Yonezawa at Tokyo University of Agriculture for his valuable discussion about genetic evolution of Bifidobacterium. The authors are indebted for the sampling to Juichi Yamagiwa (Kyoto University), Yuji Takenoshita (Chubu Gakuin University), Shiho Fujita (Kagoshima University), Ludovic Ngok Banak and Alfred Ngomanda, the former and the actual Director of the Research Institute of Tropical Ecology (IRET)/National Center of Scientific Research and Technology (CENAREST) of Gabonese Republic. Takahiro Segawa was supported by Transdisciplinary Research Integration Center (TRIC) of the Research Organization of Information and Systems. Ortholog analyses were supported by Basis for Supporting Innovative Drug Discovery and Life Science Research program (2051). Computations were partially performed on the NIG (National Institute of Genetics) supercomputer at ROIS (Research Organization of Information and Systems) National Institute of Genetics.Peer reviewe

Organic fertilizer significantly mitigates N2O emissions while increase contributed of comammox Nitrospira in paddy soils

Peer reviewe

Genomic Analyses of Bifidobacterium moukalabense Reveal Adaptations to Frugivore/Folivore Feeding Behavior

Despite the essential role of Bifidobacterium in health-promoting gut bacteria in humans, little is known about their functions in wild animals, especially non-human primates. It is difficult to determine in vivo the function of Bifidobacterium in wild animals due to the limited accessibility of studying target animals in natural conditions. However, the genomic characteristics of Bifidobacterium obtained from the feces of wild animals can provide insight into their functionality in the gut. Here, we analyzed the whole genomes of 12 B. moukalabense strains isolated from seven feces samples of wild western lowland gorillas (Gorilla gorilla gorilla), three samples of wild central chimpanzees (Pan troglodytes troglodytes) and two samples of wild forest elephants (Loxodonta cyclotis) in Moukalaba-Doudou National Park, Gabon. In addition, we analyzed the fecal bacterial communities of six wild western lowland gorillas by meta 16S rRNA gene analyses with next generation sequencing. Although the abundance of the genus Bifidobacterium was as low as 0.2% in the total reads, a whole genome analysis of B. moukalabense suggested its contribution digestion of food and nutrition of frugivore/folivore animals. Specifically, the whole genome analysis indicated the involvement of B. moukalabense in hemicellulose degradation for short chain fatty acid production and nucleic acid utilization as nitrogen resources. In comparison with human-associated Bifidobacterium spp., genes for carbohydrate transport and metabolism are not conserved in these wild species. In particular the glycosidases, which are found in all 12 strains of B. moukalabense, were variably detected, or not detected, in human-associated species.</jats:p

Genomic recovery from rare terrestrial microbes enabled by DNA-based GC-fractionation

Genome reconstruction from metagenomic samples has dramatically increased our understanding of uncultivated lineages of life. However, untargeted metagenomic sequencing is biased towards the more abundant microbes, neglecting less abundant lineages playing important ecological roles, such as the ammonia-oxidising archaea. Here, we demonstrate that separating soil molecular DNA using a bisbenzimide-CsCl guanine-cytosine (GC)-content-based DNA fractionation approach separates microbial DNA along a GC-content gradient. The fractions from both extremes of the GC-content gradient possess different 16S rRNA gene composition than the original unfractionated DNA. The high diversity in the lower GC-content fractions (&lt; 45%) contrasts with the higher DNA abundance in the higher GC-content fractions (50%–70%), highlighting the low GC fractions as an enriched source of rare microbe DNA. Metagenomic sequencing of specific low- and high-GC fractions enabled the reconstruction of 204 taxonomically diverse metagenome-assembled genomes from 31 microbial phyla, with at least 63 of these originating from rare (&lt; 0.1% relative abundance) or very rare (&lt; 0.01% relative abundance) microbial families. Therefore, this approach facilitates genomic assembly of rare taxa in resulting pseudo-communities. Ultimately, this technique enables a semi-targeted metagenomic approach to recover genomes from low-abundance microbes with GC-contents that differ significantly from the environmental microbial community of interest. As mounting evidence suggests that rare microbes drive critical ecosystem functions, this approach will facilitate a deeper understanding of their metabolic potential in the environment

Genomic Analyses of <em>Bifidobacterium moukalabense</em> Reveal Adaptations to Frugivore/Folivore Feeding Behavior

Despite the essential role of Bifidobacterium in health-promoting gut bacteria in humans, little is known about their functions in wild animals, especially non-human primates. It is difficult to determine in vivo the function of Bifidobacterium in wild animals due to the limited accessibility of studying target animals in natural conditions. However, the genomic characteristics of Bifidobacterium obtained from the feces of wild animals can provide insight into their functionality in the gut. Here, we analyzed the whole genomes of 12 B. moukalabense strains isolated from seven feces samples of wild western lowland gorillas (Gorilla gorilla gorilla), three samples of wild central chimpanzees (Pan troglodytes troglodytes) and two samples of wild forest elephants (Loxodonta cyclotis) in Moukalaba-Doudou National Park, Gabon. In addition, we analyzed the fecal bacterial communities of six wild western lowland gorillas by meta 16S rRNA gene analyses with next generation sequencing. Although the abundance of the genus Bifidobacterium was as low as 0.2% in the total reads, a whole genome analysis of B. moukalabense suggested its contribution digestion of food and nutrition of frugivore/folivore animals. Specifically, the whole genome analysis indicated the involvement of B. moukalabense in hemicellulose degradation for short chain fatty acid production and nucleic acid utilization as nitrogen resources. In comparison with human-associated Bifidobacterium spp., genes for carbohydrate transport and metabolism are not conserved in these wild species. In particular the glycosidases, which are found in all 12 strains of B. moukalabense, were variably detected, or not detected, in human-associated species