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Recent research suggests that protein deficiency symptoms are influenced by the intestinal microbiota. We investigated the influence of low protein diet on composition of the intestinal microbiota through animal experiments. Specific pathogen-free (SPF) mice were fed one of four diets (3, 6, 9, or 12% protein) for 4 weeks (n = 5 per diet). Mice fed the 3% protein diet showed protein deficiency symptoms such as weight loss and low level of blood urea nitrogen concentration in their serum. The intestinal microbiota of mice in the 3% and 12% protein diet groups at day 0, 7, 14, 21 and 28 were investigated by 16S rRNA gene sequencing, which revealed differences in the microbiota. In the 3% protein diet group, a greater abundance of urease producing bacterial species was detected across the duration of the study. In the 12% diet protein group, increases of abundance of Streptococcaceae and Clostridiales families was detected. These results suggest that protein deficiency may be associated with shifts in intestinal microbiota.

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, 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 amino acids, antioxidant activity, flavonoids and/or carotenoids in plants were optimally linked by exposure to compost. The SEM of the soil estimated that the genus Paenibacillus and nitrogen compounds 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 the 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.

Skin aging is associated with changes in cutaneous physiology including interactions with a skin microbial community. A striking alteration and diversification in the skin microbiome with aging was observed between two different age groups of 37 healthy Japanese women, i.e. younger adults of 21–37 years old and older adults of 60–76 years old, using bacterial 16S rRNA gene sequencing. The analyses revealed that the alpha diversity/species richness was significantly higher in the older than the younger group for the cheek and forehead microbiomes, while the beta diversity in the overall structure significantly differed particularly for the forearm and scalp microbiomes between the two age groups. Taxonomic profiling showed a striking reduction in the relative abundance of the majority skin genus Propionibacterium in the cheek, forearm and forehead microbiomes of the older adults, and identified 38 species including many oral bacteria that significantly differentiated the two age groups with a skin site dependency. Furthermore, we found chronological age-related and unrelated skin clinical parameters that correlate with the observed changes in the skin microbiome diversity. Thus, our data suggested that the diversification of skin microbiomes in adult women was largely affected by chronological and physiological skin aging in association with oral bacteria.

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.

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.

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, {\\delta}13C and {\\delta}15N, 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.

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.

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.

DNA transfection is an important technology in life sciences, wherein nuclear entry of DNA is necessary to express exogenous DNA. Non-viral vectors and their transfection reagents are useful as safe transfection tools. However, they have no effect on the transfection of non-proliferating cells, the reason for which is not well understood. This study elucidates the mechanism through which transfected DNA enters the nucleus for gene expression. To monitor the behavior of transfected DNA, we introduce plasmid bearing lacO repeats and RFP-coding sequences into cells expressing GFP-LacI and observe plasmid behavior and RFP expression in living cells. RFP expression appears only after mitosis. Electron microscopy reveals that plasmids are wrapped with nuclear envelope (NE)‒like membranes or associated with chromosomes at telophase. The depletion of BAF, which is involved in NE reformation, delays plasmid RFP expression. These results suggest that transfected DNA is incorporated into the nucleus during NE reformation at telophase. Haraguchi et al. investigate how transfected DNA is incorporated into the nucleus using light and electron microscopy, and the LacI/LacO system. The authors report that cytoplasmic localised plasmid DNA is incorporated into the nucleus as it reforms during M-exit and transgene expression was achieved only after nuclear reformation in the next G1.