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Maternal-offspring gut bacteriomes are closely linked to each other; however, the effects of the maternal diet have not been fully elucidated. This study aimed to determine the effect of administration of octanoate, a medium-chain fatty acid as a physiological regulator, on the fecal bacteriome and physiological indices of dams and their calves as a livestock animal model. Twelve Japanese Black cattle were randomly assigned to CON (without Ca-octanoate supplementation, n  = 6) or OCT (with Ca-octanoate supplementation, n  = 6), 60 days prior to the expected parturition date. A tendency towards enhanced feed efficiency was observed during the suckling period in OCT calves compared to CON calves, although the management of the calves was uniform from birth. Three types of machine learning algorithms computationally selected the feature factors of dams and their calves (30 d and 180 d of age). Based on the feature selection, causal inference estimated that feeding octanoate to dams would establish a positive association with the genus Bacteroides , a producer of short-chain fatty acids, at 30 d and a negative association with the genus Candidatus Stoquefichus , which is involved in colitis, at 180 d. These findings highlight that feeding octanoate to dams may influence the bacteriome of calves, thereby improving their feed efficiency.

Background The gut bacteriome influences host metabolic and physiological functions. However, its relationship with reproductive performance remains unclear. In this study, we evaluated the relationship between the gut bacteriome and reproductive performance in beef cattle, such as Japanese black heifers. Artificial insemination (AI) was performed after 300 days of age, and the number of AI required for pregnancy (AI number) was evaluated. The relationship of the fecal bacteriome at 150 and 300 days of age and reproductive performance was visualized using statistical structural equation modelling between traits based on four types of machine-learning algorithms (linear discriminant analysis, association analysis, random forest, and XGBoost). Results The heifers were classified into superior (1.04 ± 0.04 cycles, n  = 26) and inferior groups (3.87 ± 0.27 cycles, n  = 23) according to the median frequency of AI. The fecal bacteria of the two groups were examined and compared using differential analysis, which demonstrated that the genera Rikenellaceae RC9 gut group and Christensenellaceae R-7 group were increased in the superior group. Subsequently, correlation analysis evaluated the interrelationships between bacteriomes, which demonstrated that the patterns exhibited distinct characteristics. Therefore, four machine-learning algorithms were employed to identify the distinctive factors between the two groups. The directed acyclic graphs carried out by DirectLiNGAM based on these extracted factors inferred that the family Erysipelotrichaceae and the genera Clostridium sensu stricto 1 and Family XIII AD3011 group at 150 days of age were strongly associated with an increase in AI number. Furthermore, a pathway involved in creatinine degradation (PWY-4722) at 150 days of age was related to an increase in AI number. However, bacteriomes and/or pathways at 300 days of age were not necessarily related to AI number. Conclusions In this study, a causal inference methodology was applied to investigate AI-dependent gut bacterial communities in pregnant cattle. These findings suggest that AI numbers, which are crucial for beef cattle production management, could be inferred from the fecal bacterial patterns nearly six months before the AI, rather than immediately before. This study provides a novel perspective of the gut environment and its role in reproductive performance. Graphical Abstract

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.

Background Heat stress (HS) adversely affects poultry health and productivity. Recently, it has been suggested that the gut microbiota may play a role in host resilience to HS, although the details of its mechanism remain unclear. Here, the heat tolerance-related effects of dietary supplementation of compost fermented by the thermophile Bacillaceae were explored using a laying hen model (601,474 hens in total). Results In a field study conducted during the summer (maximum temperatures of approximately 35 °C) in eleven hen houses, oral administration of the compost extract resulted in a statistically significant reduction in mortality. Difference-in-differences analysis revealed that the abundances of the genera Lachnospiraceae NK3A20 group, Enterococcus , Ruminococcus 2, Blautia , Lactobacillus , Christensenellaceae R-7 group, and Tyzzerella 4 were significantly increased by compost administration, whereas those of the Prevotellaceae NK3B31 group, Prevotella 9, Romboutsia , Turicibacter , and Escherichia–Shigella were significantly reduced. In addition, to evaluate the relationship between short-chain fatty acids (SCFAs) metabolic profiles and the gut bacterial population, factor analysis combined with feature selection based on multiple machine learning (ML) algorithms was performed. The resulting optimal structural equation model suggested that compost administration led to increases in the levels of the SCFAs acetate and butyrate, as well as decreases in the levels of the genera Romboutsia and Turicibacter . Conclusion Oral administration of thermophile-fermented compost to laying hens alleviated HS-induced mortality. Integrative computational evaluations further revealed that the reduction in mortality was linked to structural changes in the gut microbiota composition and SCFA concentrations.

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.

Gadolinium (Gd) is a member of a group of rare earth metals known as lanthanides. It has been used for superconductors, magnets, fluorescent materials, electric materials, glass additives and so on. It has been also used as a paramagnetic contrast-enhancing agent in nuclear magnetic resonance imaging (MRI). It is possible that ecosystems will be damaged by the increasing industrial and medical use of gadolinium. However, there are few trials for ecological evaluation of gadolinium toxicity, especially at the community-level. This paper therefore investigated effects of gadolinium on an aquatic microbial microcosm and its pure-culture systems. The aim was: (1) to certify whether some effects observed in the microcosm exposed to gadolinium were community-level responses; and (2) to evaluate ecotoxicity of gadolinium to aquatic microbial communities compared with other heavy metals.