Body-size Scaling is Related to Gut Microbial Diversity, Metabolism and Dietary Niche of Arboreal Folivorous Flying Squirrels

Distinct Gut Microbial Enterotypes and Functional Dynamics in Wild Striped Field Mice (Apodemus agrarius) across Diverse Populations

Rodents, including the striped field mouse (Apodemus agrarius), play vital roles in ecosystem functioning, with their gut microbiota contributing significantly to various ecological processes. Here, we investigated the structure and function of 94 wild A. agrarius individuals from 7 geographic populations (45°57' N, 126°48' E; 45°87' N, 126°37' E; 45°50' N, 125°31' E; 45°59' N, 124°37' E; 46°01' N, 124°88' E; 46°01' N, 124°88' E; 46°01' N, 124°88' E), revealing two distinct enterotypes (Type1 and Type2) for the first time. Each enterotype showed unique microbial diversity, functions, and assembly processes. Firmicutes and Bacteroidetes dominated, with a significant presence of Lactobacillus and Muribaculaceae. Functional analysis highlighted metabolic differences, with Type1 emphasizing nutrient processing and Type2 showing higher energy production capacity. The analysis of the neutral model and the null model revealed a mix of stochastic (drift and homogenizing dispersal) and deterministic processes (homogenous selection) that shape the assembly of the microbiota, with subtle differences in the assembly processes between the two enterotypes. Correlation analysis showed that elevation and BMI were associated with the phylogenetic turnover of microbial communities, suggesting that variations in these factors may influence the composition and diversity of the gut microbiota in A. agrarius. Our study sheds light on gut microbial dynamics in wild A. agrarius populations, highlighting the importance of considering ecological and physiological factors in understanding host-microbiota interactions.

Geographical distribution and species variation of gut microbiota in small rodents from the agro-pastoral transition ecotone in northern China

The gut microbiota of rodents is essential for survival and adaptation and is susceptible to various factors, ranging from environmental conditions to genetic predispositions. Nevertheless, few comparative studies have considered the contribution of species identity and geographic spatial distance to variations in the gut microbiota. In this study, a random sampling survey encompassing four rodent species (Apodemus agrarius, Cricetulus barabensis, Tscherskia triton and Rattus norvegicus) was conducted at five sites in northern China's farming-pastoral ecotone. Through a cross-factorial comparison, we aimed to discern whether belonging to the same species or sharing the same capture site predominantly influences the composition of gut microbiota. Notably, the observed variations in microbiome composition among these four rodent species match the host phylogeny at the family level but not at the species level. The gut microbiota of these four rodent species exhibited typical mammalian characteristics, predominantly characterized by the Firmicutes and Bacteroidetes phyla. As the geographic distance between populations increased, the number of shared microbial taxa among conspecific populations decreased. We observed that within a relatively small geographical range, even different species exhibited convergent α-diversity due to their inhabitation within the same environmental microbial pool. In contrast, the composition and structure of the intestinal microbiota in the allopatric populations of A. agrarius demonstrated marked differences, similar to those of C. barabensis. Additionally, geographical environmental elements exhibited significant correlations with diversity indices. Conversely, host-related factors had minimal influence on microbial abundance. Our findings indicated that the similarity of the microbial compositions was not determined primarily by the host species, and the location of the sampling explained a greater amount of variation in the microbial composition, indicating that the local environment played a crucial role in shaping the microbial composition.

Plant rhizosphere defense system respond differently to emerging polyfluoroalkyl substances F-53B and PFOS stress

Chlorinated polyfluoroalkyl ether sulfonate (F-53B) and perfluorooctanesulfonate (PFOS) are used and emitted as fog inhibitors in the chromium plating industry, and they are widely detected worldwide. To study the effects of F-53B and PFOS on the rhizosphere defense system, they were added at two levels (0.1 and 50 mg L^-1) to the soil where different plants (Lythrum salicaria and Phragmites communis) were grown. In bulk soils, high concentrations of F-53B/PFOS resulted in significant increases in soil pH, NH₄⁺-N, and NO₃^--N (the effect of PFOS on NO₃^--N was not significant). Moreover, the extent of the effects of PFOS and F-53B on the physicochemical properties of bulk soils were different (e.g., PFOS caused an increase of NH₄⁺-N by 8.94%-45.97% compared to 1.63%-25.20% for F-53B). Root exudates and PFASs together influenced the physicochemical properties of rhizosphere soils (e.g., TOC increased significantly in contaminated rhizosphere soils but did not change in non-bulk soils). Under the influence of F-53B/PFOS, the root exudates regulated by plants were changed and weakened the effect of F-53B/PFOS on microbial community of rhizosphere soil. The rhizosphere defense systems of different plants have both similarities and differences in response to different substances and concentrations.

Aeromonas hydrophila Induces Skin Disturbance through Mucosal Microbiota Dysbiosis in Striped Catfish (Pangasianodon hypophthalmus)

Bacterial pathogens are well equipped to adhere to and initiate infection in teleost fish. Fish skin mucus serves as the first barrier against environmental pathogens. The mucus harbors commensal microbes that impact host physiological and immunological responses. However, how the skin mucosal microbiota responds to the presence of pathogens remains largely unexplored. Thus, little is known about the status of skin mucus prior to infection with noticeable symptoms. In this study, we investigated the interactions between pathogens and the skin mucosal microbiota as well as the fish skin immune responses in the presence of pathogens. Striped catfish (Pangasianodon hypophthalmus) were challenged with different concentrations of the bacterial pathogen Aeromonas hydrophila (AH), and the skin immune response and the mucosal microbiota were examined by quantitative PCR (qPCR) and 16S rRNA gene sequence analysis. We determined that the pathogen concentration needed to stimulate the skin immune response was associated with significant mucosal microbiota changes, and we reconfirmed these observations using an ex vivo fish skin model. Further analysis indicated that changes in the microbiota were attributed to a significant increase in opportunistic pathogens over AH. We concluded that the presence and increase of AH result in dysbiosis of the mucosal microbiota that can stimulate skin immune responses. We believe that our work sheds light on host-pathogen-commensal microbiota interactions and therefore contributes to aquaculture fish health.

IMPORTANCE The fish skin mucosal microbiota is essential in modulating the host response to the presence of pathogens. Our study provides a platform to study both the correlation and causation of the interactions among the pathogen, fish skin, and the skin mucosal microbiota. Based on these findings, we provide the first mechanistic information on how mucosal microbiota changes induced by the pathogen AH result in skin disturbance with immune stimulation in striped catfish in the natural state and a potential direction for early-infection screening. Thus, this study is highly significant in the prevention of fish disease.

Bacterial Dynamics in the Accessory Nidamental Gland of Sepioteuthis lessoniana throughout Maturation

The accessory nidamental gland (ANG) is part of the reproduction organ in the majority of female cephalopods, including the bigfin reef squid Sepioteuthis lessoniana, an economically important fishery product. Microbes in Alphaproteobacteria, Gammaproteobacteria, and Verrucomicrobia have been suggested to play a role in the maturation of the S. lessoniana ANG and are responsible for its color. However, the bacterial composition and dynamics of the different maturation stages of the ANG remain unclear. In the present study, we surveyed ANG-associated bacterial dynamics in wild-caught S. lessoniana at various developmental stages in different populations over 3 years. The results obtained showed that the ANG bacterial community shifted gradually and decreased in diversity throughout maturation. Verrucomicrobia occupied the ANG during the early stages in large numbers, and was replaced by Bacteroidia, Alphaproteobacteria, and Gammaproteobacteria in the later stages. Flavobacteriales and Alphaproteobacteria both appeared to contribute to pigmentation, while Bacteroidia, Alphaproteobacteria, and Gammaproteobacteria may be involved in enriching the heme biosynthesis pathway in the ANG with the maturation of S. lessoniana. The present results provide an open question of whether S. lessoniana actively selects the bacterial community in the ANG to adjust to its surrounding environment.

Host phylogeny and host ecology structure the mammalian gut microbiota at different taxonomic scales

The gut microbiota is critical for host function. Among mammals, host phylogenetic relatedness and diet are strong drivers of gut microbiota structure, but one factor may be more influential than the other. Here, we used 16S rRNA gene sequencing to determine the relative contributions of host phylogeny and host diet in structuring the gut microbiotas of 11 herbivore species from 5 families living sympatrically in southwest Kenya. Herbivore species were classified as grazers, browsers, or mixed-feeders and dietary data (% C4 grasses in diet) were compiled from previously published sources. We found that herbivore gut microbiotas were highly species-specific, and that host taxonomy accounted for more variation in the gut microbiota (30%) than did host dietary guild (10%) or sample month (8%). Overall, similarity in the gut microbiota increased with host phylogenetic relatedness (r = 0.74) across the 11 species of herbivores, but among 7 closely related Bovid species, dietary %C4 grass values more strongly predicted gut microbiota structure (r = 0.64). Additionally, within bovids, host dietary guild explained more of the variation in the gut microbiota (17%) than did host species (12%). Lastly, while we found that the gut microbiotas of herbivores residing in southwest Kenya converge with those of distinct populations of conspecifics from central Kenya, fine-scale differences in the abundances of bacterial amplicon sequence variants (ASVs) between individuals from the two regions were also observed. Overall, our findings suggest that host phylogeny and taxonomy strongly structure the gut microbiota across broad host taxonomic scales, but these gut microbiotas can be further modified by host ecology (i.e., diet, geography), especially among closely related host species.

Breeding farm, level of feeding and presence of antibiotics in the feed influence rabbit cecal microbiota

Background

The effect of the production environment and different management practices in rabbit cecal microbiota remains poorly understood. While previous studies have proved the impact of the age or the feed composition, research in the breeding farm and other animal management aspects, such as the presence of antibiotics in the feed or the level of feeding, is still needed. Characterization of microbial diversity and composition of growing rabbits raised under different conditions could help better understand the role these practices play in cecal microbial communities and how it may result in different animal performance.

Results

Four hundred twenty-five meat rabbits raised in two different facilities, fed under two feeding regimes (ad libitum or restricted) with feed supplemented or free of antibiotics, were selected for this study. A 16S rRNA gene-based assessment through the MiSeq Illumina sequencing platform was performed on cecal samples collected from these individuals at slaughter. Different univariate and multivariate approaches were conducted to unravel the influence of the different factors on microbial alpha diversity and composition at phylum, genus and OTU taxonomic levels. The animals raised in the facility harboring the most stable environmental conditions had greater, and less variable, microbial richness and diversity. Bootstrap univariate analyses of variance and sparse partial least squares-discriminant analyses endorsed that farm conditions exerted an important influence on rabbit microbiota since the relative abundances of many taxa were found differentially represented between both facilities at all taxonomic levels characterized. Furthermore, only five OTUs were needed to achieve a perfect classification of samples according to the facility where animals were raised. The level of feeding and the presence of antibiotics did not modify the global alpha diversity but had an impact on some bacteria relative abundances, albeit in a small number of taxa compared with farm, which is consistent with the lower sample classification power according to these factors achieved using microbial information.

Conclusions

This study reveals that factors associated with the farm effect and other management factors, such as the presence of antibiotics in the diet or the feeding level, modify cecal microbial communities. It highlights the importance of offering a controlled breeding environment that reduces differences in microbial cecal composition that could be responsible for different animal performance.