Biology subjects

Shimasaki, T.

Publications and source records attributed to Shimasaki, T..

4 recordsLinked to original sources

bioRxiv2026

Effects of periodic group housing opportunities on reproductive performance and welfare in sows

ObjectiveStall housing of pregnant sows raises welfare concerns, whereas conventional group housing systems often reduce space efficiency. This study evaluated the effects of periodic group housing (PG) on reproductive performance and welfare compared with continuous stall housing (CS). MethodsSows in the CS group (n = 15) were continuously housed in stalls. In the PG group (n = 15), sows were housed in groups of three and allocated 1 day of group housing and 6 days of stall housing per week over 10 weeks. During group housing sessions, the sows had access to a group housing area containing sawdust. Behavioral observations and salivary cortisol measurements were conducted on the first day of the stall housing session in weeks 1, 6, and 10. Behavioral indices were expressed as proportions based on 90 sampling points recorded at 1-min intervals. ResultsThe number of stillbirths was significantly lower in the PG group than in the CS group (0.63 vs. 1.49 piglets per litter). whereas other reproductive outcomes, including total litter size and average birth weight, did not differ. In older parity sows, the PG treatment markedly increased the proportion of time spent lying, suggesting reduced discomfort associated with restricted movement. Furthermore, the proportion of exploratory behavior decreased markedly, and drinking behavior showed a decreasing trend across parity levels in the PG group, suggesting partial satisfaction of motivations for environmental exploration and oral manipulation. The proportion of oral abnormal behavior showed a pronounced interaction between housing treatment and experimental week, increasing from week 1 to week 6 in the PG group. Salivary cortisol concentrations did not differ between the groups. ConclusionPG may improve reproductive performance and partially satisfy the behavioral motivations restricted under continuous stall housing. This system may represent a practical alternative for improving animal welfare while minimizing economic losses.

animal behavior and cognition↗

bioRxiv2025

Horizontal acquisition of nicotine catabolism gene cluster drives the assembly of tobacco root microbiota community

BackgroundPlant roots are hotspots for interactions with soil microbes, where a characteristic bacterial community structure is formed. Plant specialized metabolites often play pivotal roles in this assembly process. However, the molecular basis underlying root microbiota responses to these bioactive compounds, and how such metabolic interactions shape the assembly of host-specific root microbiota, remain largely unknown. Nicotine is a toxic alkaloid predominantly produced by the genus Nicotiana, and the genus Arthrobacter is known as one of the nicotine-degrading bacteria in the tobacco root microbiota. In this study, we used the tobacco-Arthrobacter interaction system as a model and integrated comparative genomics and experimental genetic manipulation assays to uncover the role of bacterial catabolism capacity for host specialized metabolites in shaping host-specific root microbiota. ResultsNicotine catabolism genes are uniquely found in the Arthrobacter strains derived from nicotine-containing environments, and this restricted gene distribution is driven by a plasmid-mediated horizontal gene transfer. To assess the ecological consequences of this genomic adaptation in Arthrobacter fitness in tobacco roots, we conducted adaptation assays under both in vitro and in planta conditions using genetically manipulated Arthrobacter and tobacco mutants, which are impaired in nicotine catabolism and biosynthesis, respectively. Nicotine improves Arthrobacter colonization to the tobacco roots through both catabolism-dependent and catabolism-independent mechanisms. Bacterial community analysis using a synthetic community approach further demonstrated that these metabolic interactions, mediated by tobacco nicotine biosynthesis and its catabolism by Arthrobacter, jointly affect root microbiota composition. ConclusionsOur findings illustrated that bacterial catabolic capacity toward host-derived plant specialized metabolites is key for successful root colonization. This metabolic adaptation is driven by plasmid-mediated horizontal gene transfer and ultimately shapes the structure of the overall root microbiota community.

microbiology↗

bioRxiv2023

Discovery of an isoflavone oxidative catabolic pathway in legume root microbiota

Isoflavones are major specialized metabolites found in legume plants, where they contribute to environmental adaptation. Isoflavones also play a role human health as promising therapeutic agents. This metabolite group is involved in interactions with soil microorganisms as initiation signals in rhizobial symbiosis and as modulators of the legume root microbiota. We previously reported that isoflavones enrich the Comamonadaceae, a predominant bacterial family in soybean roots, and that microorganisms in legume rhizosphere soil degrade isoflavones. However, the isoflavone catabolism pathway that underly the isoflavone-mediated legume-microbiota interactions have not yet been clarified. Here, we isolated Variovorax sp. strain V35, member of the Comamonadaceae that harbors isoflavone-degrading activity, from soybean roots and discovered a gene cluster responsible for isoflavone degradation named ifc. Strain V35 metabolizes isoflavones in a completely distinct oxidative manner from the reductive isoflavone metabolism pathway elucidated in the gut microbiota, in which resulting products enter the tricarboxylic acid cycle. The characterization of ifc mutants and heterologously expressed IFC enzymes revealed that isoflavones are catabolized via A-ring cleaving fission, which starts with hydroxylation at the 8-position of the A-ring. We further demonstrated that ifc genes are frequently found in bacterial strains isolated from legume plants, including mutualistic rhizobia, and contribute to detoxification of the antibacterial activity of isoflavones. Taken together, our findings reveal an oxidative catabolism pathway of isoflavone in the soybean root microbiota, providing molecular insights into isoflavone-mediated legume-microbiota interactions. SignificanceIsoflavones play pivotal roles in plant-environment interactions and in the maintenance and improvement of human health. Bacterial metabolism is a fundamental component of isoflavone-mediated interkingdom interactions. In the human gut, intestinal bacteria convert isoflavones into equol, a highly bioactive compound. However, the fate of isoflavones in the legume rhizosphere has not been elucidated, despite them being the key signaling molecules for nodule symbiosis and modulation of the legume root microbiota. Here, we discovered a novel isoflavone catabolism pathway in the soybean root microbiota and demonstrated the strong association between bacterial catabolic abilities and their interactions with host plants. Collectively, our findings provide new insights into bacterial isoflavone metabolism and a molecular understanding of legume-microbiota interactions.

plant biology↗

bioRxiv2020

Species-specific assembly of root-associated bacterial microbiota mediated by a combination of plant specialized metabolites

Plant specialized metabolites (PSMs) influence the taxonomic compositions of the root-associated microbiota; however, the underlying molecular mechanisms and evolutionary trajectories remain elusive. Here, we show that the bacterial genus Arthrobacter is predominant in the tobacco endosphere, and that its enrichment is mediated by a combination of two tobacco-specific PSMs, santhopine and nicotine The isolation and whole genome sequencing of a representative set of Arthrobacter strains identified independent genomic features, including but not limited to genes for santhopine and nicotine catabolism, which are associated with the colonization competence of tobacco roots. Taken together, these data suggest that plant species-specific root microbiota assembly is mediated by bacterial catabolism of a cocktail of PSMs synthesized by the host plant.

microbiology↗