arXiv subjects

Naoko Tsuji

Publications and source records attributed to Naoko Tsuji.

7 recordsLinked to original sources

arXiv2026

A putative model of the gut-muscle axis in aged livestock

The gut-muscle axis has been proposed to link gut microbiota with skeletal muscle physiology, yet its universality across livestock species remains unclear. Using aged laying hens, a livestock model with a relatively short digestive tract, we examined the gut microbiota, faecal metabolome, and breast-muscle metabolome by integrative multi-omics analyses in hens fed a Caldifermentibacillus hisashii-containing fermented feed or a control diet. Non-metric multidimensional scaling revealed clear separation of the microbial community between groups (stress = 0.0097), characterised by a marked expansion of Lactobacillus with the administration of the fermented feed. Variance partitioning showed that the 16S microbiota shared substantial variance with both the faecal (shared R2 adj = 0.54) and muscle (shared R2 adj = 0.48) metabolomes, and partial dbRDA demonstrated that the faecal-to-muscle metabolite association was largely retained after controlling for 16S (direct R2 = 0.538, partial R2 = 0.485), consistent with faecal metabolites acting as an integral layer linking microbiota to muscle. Cliff's delta-based selection showed depletion of proteolytic taxa and faecal amino acids, and reduced muscle Ornithine and uric acid alongside elevated Hypoxanthine. Because both groups were processed identically post-slaughter, these differences reflect in vivo states: amino acid depletion despite reduced bacterial proteolytic capacity points to enhanced host utilisation, and reduced uric acid, a post-mortem-stable purine end-product in uricotelic chickens, indicates efficient nitrogen turnover rather than accumulation. Collectively, these findings support a putative tripartite model of the gut-muscle axis in aged laying hens, providing a statistically grounded framework for understanding microbial contributions to muscle physiology in aged livestock.

q-bio.TO↗

arXiv2026

A novel sustainable role of compost as a universal protective substitute for fish, chicken, pig, and cattle, and its estimation by structural equation modeling

Natural decomposition of organic matter is essential in food systems, and compost is used worldwide as an organic fermented fertilizer. However, as a feature of the ecosystem, its effects on the animals are poorly understood. Here we show that oral administration of compost and/or its derived thermophilic Bacillaceae, i.e., Caldibacillus hisashii and Weizmannia coagulans, can modulate the prophylactic activities of various industrial animals. The fecal omics analyses in the modulatory process showed an improving trend dependent upon animal species, environmental conditions, and administration. However, structural equation modeling (SEM) estimated the grouping candidates of bacteria and metabolites as standard key components beyond the animal species. In particular, the SEM model implied a strong relationship among partly digesting fecal amino acids, increasing genus Lactobacillus as inhabitant beneficial bacteria and 2-aminoisobutyric acid involved in lantibiotics. These results highlight the potential role of compost for sustainable protective control in agriculture, fishery, and livestock industries.

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arXiv2025

Symbiotic causal network of seagrass-bacteria-algae-diatoms interactions

Seagrass meadows contribute to the conservation of marine ecosystems, reduction in global warming impacts and pathogen controls. However, the decline in seagrass habitats due to environmental loads has become an urgent global issue. One way to address this issue is to better understand healthy seagrass habitats. Here, we estimate the structural characteristics of symbiotic and metabolic systems in sediments from eight coastal regions of Japan, with each region containing both seagrass-covered areas and adjacent unvegetated areas. Notably, seagrasses commonly maintain a balanced symbiotic relationship characterized by a positive association with cable bacteria (Desulfobulbaceae), nitrogen-cycling bacteria (Hyphomonadaceae), and coral algae (Corallinophycidae) and a negative association with diatoms (Diatomea). Furthermore, seagrass growth conditions influence metabolic pathways by activating nitrogen-related metabolism while attenuating methanogenesis. Our findings highlight the crucial roles of marine plants and their symbiotic systems in ensuring environmental conservation within the context of blue carbon storage across environmental gradients.

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arXiv2023

Antibiotic-dependent instability of homeostatic plasticity for growth and environmental load

Reducing antibiotic usage in livestock animals has become an urgent issue worldwide to prevent antimicrobial resistance. Here, abuse of chlortetracycline (CTC), a versatile antibacterial agent, on the performance, blood components, fecal microbiota, and organic acid concentration in calves was investigated. Japanese Black calves were fed milk replacer containing CTC at 10 g/kg (CON) or 0 g/kg (EXP). Growth performance was not affected by CTC administration. However, CTC administration altered the correlation between fecal organic acids and bacterial genera. Machine learning methods such as association analysis, linear discriminant analysis, and energy landscape analysis revealed that CTC administration affected according to certain rules the population of various types of fecal bacteria. It is particularly interesting that the population of several methane-producing bacteria was high in the CON, and that of Lachnospiraceae, a butyrate-producing bacteria, was high in the EXP at 60 d of age. Furthermore, statistical causal inference based on machine learning data estimated that CTC treatment affects the entire intestinal environment, inhibiting butyrate production for growth and biological defense, which may be attributed to methanogens in feces. Thus, these observations highlight the multiple harmful impacts of antibiotics on intestinal health and the potential production of greenhouse gas in the calves.

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arXiv2023

Agricultural quality matrix-based multiomics structural analysis of carrots in soils fertilized with thermophile-fermented compost

Compost is used worldwide as a soil conditioner for crops, but its functions have still been explored. Here, the omics profiles of carrots were investigated, as a root vegetable plant model, in a field amended with compost fermented with thermophilic Bacillaceae for growth and quality indices. Exposure to compost significantly increased the productivity, antioxidant activity, red color, and taste of the carrot root and altered the soil bacterial composition with the levels of characteristic metabolites of the leaf, root, and soil. Based on the data, structural equation modeling (SEM) estimated that L-2-aminoadipate, phenylalanine, flavonoids and / or carotenoids in plants were optimally linked by exposure to compost. The SEM of the soil estimated that the genus Paenibacillus, L-2-aminoadipate and nicotinamide, and S-methyl L-cysteine were optimally involved during exposure. These estimates did not show a contradiction between the whole genomic analysis of compost-derived Paenibacillus isolates and the bioactivity data, inferring the presence of a complex cascade of plant growth-promoting effects and modulation of the nitrogen cycle by compost itself. These observations have provided information on the qualitative indicators of compost in complex soil-plant interactions and offer a new perspective for chemically independent sustainable agriculture through the efficient use of natural nitrogen.

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arXiv2022

Estimation of symbiotic bacterial structure in a sustainable seagrass ecosystem on recycled management

Seagrass meadows play an essential role in blue carbon and aquatic ecosystem services. However, methods for the flourishing of seagrass are still being explored. Here, data from 49 public coastal surveys on the distribution of seagrass and seaweed around the onshore aquaculture facilities are revalidated, and an exceptional area where the seagrass Zostera marina thrives was found. The bacterial population there showed an apparent decrease in the pathogen candidates belonging to the order Flavobacteriales. Moreover, structure equation modeling and a linear non-Gaussian acyclic model based on the machine learning data estimated an optimal symbiotic bacterial group candidate for seagrass growth as follows: the Lachnospiraceae and Ruminococcaceae families as gut-inhabitant bacteria, Rhodobacteraceae as photosynthetic bacteria, and Desulfobulbaceae as cable bacteria modulating oxygen or nitrate reduction and oxidation of sulfide. These observations confer a novel perspective on the seagrass symbiotic bacterial structures critical for blue carbon and low-pathogenic marine ecosystems in aquaculture.

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arXiv2022

Symbiotic bacterial network structure involved in carbon and nitrogen metabolism of wood-utilizing insect larvae

Effective biological utilization of wood biomass is necessary worldwide. Since several insect larvae can use wood biomass as a nutrient source, studies on their digestive mechanism are expected to speculate a novel rule in wood biomass processing. Here, the relationships of inhabitant bacteria involved in carbon and nitrogen metabolism in the intestine of beetle larvae, an insect model, are investigated. Bacterial analysis of larval feces showed enrichment of members of which could include candidates for plant growth promotion, nitrogen cycle modulation, and/or environmental protection. The abundances of these bacteria were not necessarily positively correlated with the abundance in the habitat, suggesting that they might be selectively enriched in the intestines of larvae. Further association analysis predicted that carbon and nitrogen metabolism in the intestine was affected by the presence of the other common bacteria, the populations of which were not remarkably altered in the habitat and feces. Based on hypotheses targeting these selected bacterial groups, structural estimation modeling analyses statistically suggested that their metabolism of carbon and nitrogen and their stable isotopes, δ13C and δ15N, may be associated with fecal enriched bacteria and other common bacteria. In addition, other causal inference analyses, such as causal mediation analysis, linear non-Gaussian acyclic model (LiNGAM), and BayesLiNGAM, did not necessarily affirm the existence of prominent bacteria involved in metabolism, implying its importance as the bacterial groups for metabolism rather than a remarkable bacterium. Thus, these observations highlight a multifaceted view of symbiotic bacterial groups utilizing carbon and nitrogen from wood biomass in insect larvae as a cultivator of potentially environmentally beneficial bacteria.

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