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

A retrospective analysis of antimicrobial resistance in pathogenic Escherichia coli and Salmonella spp. isolates from poultry in Uganda

There are increasing reports of antimicrobial treatment failures for bacterial diseases of poultry in Uganda. The paucity of data on antimicrobial resistance (AMR) of pathogenic bacteria in Uganda is a major setback to AMR control. This study investigated the occurrence of fowl typhoid, colibacillosis, and AMR in associated pathogens from 2012 to 2018. Laboratory records from the Central Diagnostic Laboratory (CDL), a National Veterinary Diagnostic Facility located at Makerere University, were reviewed. Archived isolates of the causative bacteria for the two diseases were also evaluated for AMR. The frequencies of the two disease conditions, their clinical and necropsy presentations and the demographic data of the diagnostic samples were summarized from the records. Archived bacterial isolates were revived before antimicrobial susceptibility testing. This was done on Mueller Hinton agar using the disk diffusion method, against 16 antimicrobials of medical and veterinary importance according to the Clinical Laboratory Standards Institute guidelines. A total of 697 poultry cases were presented for bacteriological investigations in the review period. Colibacillosis and salmonellosis had prevalence rates of 39.7% (277/697) and 16.2% (113/697), respectively. A total of 63 and 92 isolates of Escherichia coli and Salmonella spp., respectively, were archived but 43 (68.3%) E. coli and 47 (51.1%) Salmonella spp. isolates were recovered and evaluated for AMR. Multidrug resistance was more frequent in E. coli (38; 88.4%) than salmonellae (25; 53.2%), (p < 0.001). The high prevalence of colibacillosis, salmonellosis and the AMR of associated pathogens warrants immediate institution of appropriate disease control measures

Isolation of bacteria from freeze-dried samples and the functional characterization of species-specific lactic acid bacteria with a comparison of wild and captive proboscis monkeys

Previously, we isolated a novel lactic acid bacteria species (Lactobacillus nasalidis) from the fresh forestomach contents of a captive proboscis monkey (Nasalis larvatus) in a Japanese zoo. In this study, we isolated two strains of L. nasalidis from the freeze-dried forestomach contents of a wild proboscis monkey inhabiting a riverine forest in Malaysia. The samples had been stored for more than six years. Phenotypic analysis showed that strains isolated from the wild individual had more diverse sugar utilization and lower salt tolerance than strains previously isolated from the captive counterpart. These phenotypic differences are most likely induced by feeding conditions; wild individuals consume a wide variety of natural food, unlike their zoo-raised counterparts that consume formula feed with sodium sufficiency. Since 16s rRNA sequences of L. nasalidis were detected in the previously created 16S rRNA libraries of wild, provisioned, and captive proboscis monkeys in Malaysia and Japan, L. nasalidis may be an essential bacterium of the foregut microbial community of the proboscis monkey. The currently established method for the isolation of gut bacteria from freeze-dried samples under storage will be applicable to many already-stored precious samples

Occurrence of Selected Bacterial Antibiotic Resistance Genes in Soils of Animal Farms in Uganda

The antibiotic resistance genes (ARG) of bacteria can be found in diverse environments such as the gut of mammals, soil, air, and water. In this research, we examined soils (for ARG) from 27 animal farms in Uganda (Mbarara, Wakiso and Mpigi districts) rearing poultry, pigs, dairy, or beef animals. Among these 27 places, there were antibiotic-free farms and those, which routinely used antibiotics to control diseases. DNA was extracted from soil samples using a commercial kit. A polymerase chain reaction (PCR) was performed to detect baScterial genes of resistance to sulphonamide (3 genes), beta lactam (1 gene), and Tetracycline (8 genes) antibiotics. The highest number of soils contaminated with these genes were from Mpigi district, whereas in Mbarara we found contamination of farm soils to a lesser extent. In all districts, the ARG were detected in farm soils regardless of the evidence of antibiotic usage; however, ARG were predominant in severe antibiotic consuming farms than the less consuming ones. Sulphonamide resistance genes were predominant in most district samples. In particular, the sul2 (Sulphonamide) and tetW (Tetracycline) genes were the most prevalent in all samples, suggesting that fecal disposal or use of animal manure could drive the accumulation of ARG in these soils, making it a deadly reservoir, especially in areas with vast consumption of antibiotics