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Simple Summary: The gut bacterial community of two captive ducks was investigated in this study across seasons. It was discovered that the composition of gut bacteria was significantly affected by seasonal variations, with greater diversity in winter. Different seasons yielded different biomarkers, with the majority found in winter when a more intricate bacterial network structure was seen. Ten important pathogenic bacterial species were discovered and appeared to be more abundant in the summer. The presence of significant pathogenic bacteria was demonstrated by this study, raising concerns for captive animals, and shedding light on how gut bacterial composition is affected by seasonal fluctuations. Vertebrates and their gut bacteria interact in complex and mutually beneficial ways. The intestinal microbial composition is influenced by several external influences. In addition to food, the abiotic elements of the environment, such as temperature, humidity, and seasonal fluctuation are also important determinants. Fecal samples were collected from two captive duck species, Baikal teal (Sibirionetta formosa) and common teal (Anas crecca) across four seasons (summer, autumn, winter, and spring). These ducks were consistently fed the same diet throughout the entire experiment. High throughput sequencing (Illumina Mi-seq) was employed to analyze the V4–V5 region of the 16sRNA gene. The dominant phyla in all seasons were Proteobacteria and Firmicutes. Interestingly, the alpha diversity was higher in winter for both species. The NMDS, PCoA, and ANOSIM analysis showed the distinct clustering of bacterial composition between different seasons, while no significant differences were discovered between duck species within the same season. In addition, LefSe analysis demonstrated specific biomarkers in different seasons, with the highest number revealed in winter. The co-occurrence network analysis also showed that during winter, the network illustrated a more intricate structure with the greatest number of nodes and edges. However, this study identified ten potentially pathogenic bacterial species, which showed significantly enhanced diversity and abundance throughout the summer. Overall, our results revealed that season mainly regulated the intestinal bacterial community composition and pathogenic bacteria of captive ducks under the instant diet. This study provides an important new understanding of the seasonal variations in captive wild ducks' intestinal bacterial community structure. The information available here may be essential data for preventing and controlling infections caused by pathogenic bacteria in captive waterbirds. [ABSTRACT FROM AUTHOR]

Simple Summary: The fungi community has received comparatively little attention compared to bacteria in previous studies on the avian gut microbiome. Even though fungi constitute a smaller proportion of the gastrointestinal (GIT) microbiota, changes in the diversity and composition of the gut microbial population have been associated with a number of diseases. This study, concentrating on captive migratory ducks, provides light on the gut fungal population, identifies potential animal pathogens and plant saprotrophs, and reveals that seasonal variations shape the dynamics of the gut fungal community more significantly than the host species. Understanding the dynamics of avian gut fungal communities and potentially pathogenic species across different seasons is crucial for assessing their health and ecological interactions. In this study, high-throughput sequencing was employed to examine the changes in gut fungal communities and the presence of potential pathogens between different seasons in captive Baikal teal and common teal. Between the summer and autumn seasons, both duck species showed significant differences in fungal diversity and community composition. A higher fungal diversity in both species was exhibited in the summer than in the autumn. Ascomycota and Basidiomycota were the two most common phyla, with a greater proportion of Ascomycota than Basidiomycota in both duck species in the summer. Interestingly, our study also identified animal pathogens and plant saprotrophs in the gut fungal communities. Seasonal variation had an effect on the diversity and abundance of both animal pathogens and saprotrophs. Specifically, during the summer season, the diversity and relative abundance were higher compared to the autumn season. In addition, there were differences between duck species in terms of animal pathogens, while no significant differences were observed in saprotrophs. Overall, the communities of the gut fungi, animal pathogens, and saprotrophs were found to be influenced by seasonal changes rather than host species. Therefore, seasonal variations might dominate over host genetics in shaping the gut microbiota of captive Baikal teal and common teal. This study underscores the importance of incorporating an understanding of seasonal dynamics and potential pathogens within the gut microbiota of captive ducks. Such considerations have the potential to drive progress in the development of sustainable and economically viable farming practices. [ABSTRACT FROM AUTHOR]

Simple Summary: The gut microbiota plays important roles for maintaining the health of the host. In this study, the results revealed significant differences in the gut bacterial communities among bean geese, hooded cranes, and domestic geese. In comparison to domestic geese, the gut bacterial community of bean geese and hooded cranes had a greater capacity for energy metabolism, suggesting that wild birds may rely more on their gut microbiota to survive in cold conditions. Furthermore, pathogens were discovered to overlap among the three hosts, reminding us to monitor the potential for pathogen transmission between poultry and wild birds. Hooded cranes showed the highest diversity and relative abundance of pathogens compared to the other two species. Due to its vulnerable status, more focus should be paid to the protection of the hooded crane species. These findings could help us gain a deeper understanding of the structure of gut bacterial and pathogenic communities in poultry and wild birds. The host's physiological well-being is intricately associated with the gut microbiota. However, previous studies regarding the intestinal microbiota have focused on domesticated or captive birds. This study used high-throughput sequencing technology to identify the gut bacterial communities of sympatric bean geese, hooded cranes, and domestic geese. The results indicated that the gut bacterial diversity in domestic geese and hooded cranes showed considerably higher diversity than bean geese. The gut bacterial community compositions varied significantly among the three hosts (p < 0.05). Compared to the hooded crane, the bean goose and domestic goose were more similar in their genotype and evolutionary history, with less difference in the bacterial community composition and assembly processes between the two species. Thus, the results might support the crucial role of host genotypes on their gut microbiota. The gut bacteria of wild hooded cranes and bean geese had a greater capacity for energy metabolism compared to domestic geese, suggesting that wild birds may rely more on their gut microbiota to survive in cold conditions. Moreover, the intestines of the three hosts were identified as harboring potential pathogens. The relative abundance of pathogens was higher in the hooded crane compared to the other two species. The hooded crane gut bacterial community assemblage revealed the least deterministic process with the lowest filtering/selection on the gut microbiota, which might have been a reason for the highest number of pathogens result. Compared to the hooded crane, the sympatric bean goose showed the least diversity and relative abundance of pathogens. The intestinal bacterial co-occurrence network showed the highest stability in the bean goose, potentially enhancing host resistance to adverse environments and reducing the susceptibility to pathogen invasion. In this study, the pathogens were also discovered to overlap among the three hosts, reminding us to monitor the potential for pathogen transmission between poultry and wild birds. Overall, the current findings have the potential to enhance the understanding of gut bacterial and pathogenic community structures in poultry and wild birds. [ABSTRACT FROM AUTHOR]

Simple Summary: Phalacrognathus muelleri is naturally distributed in Queensland (Australia) and New Guinea, and this species can be successfully bred under artificial conditions. In this study, we compared gut bacterial community structure among different life stages. There were dramatic shifts in gut bacterial community structure between larvae and adults, which was probably shaped by their diet. The significant differences between early instar and final instars larvae suggested that certain life stages are associated with a defined gut bacterial community. Our results contribute to a better understanding of the potential role of gut microbiota in a host's growth and development, and the data will benefit stag beetle conservation in artificial feeding conditions. Although stag beetles are popular saprophytic insects, there are few studies about their gut bacterial community. This study focused on the gut bacterial community structure of the rainbow stag beetle (i.e., Phalacrognathus muelleri) in its larvae (three instars) and adult stages, using high throughput sequencing (Illumina Miseq). Our aim was to compare the gut bacterial community structure among different life stages. The results revealed that bacterial alpha diversity increased from the 1st instar to the 3rd instar larvae. Adults showed the lowest gut bacterial alpha diversity. Bacterial community composition was significantly different between larvae and adults (p = 0.001), and 1st instar larvae (early instar) had significant differences with the 2nd (p= 0.007) and 3rd (p = 0.001) instar larvae (final instar). However, there was little difference in the bacterial community composition between the 2nd and 3rd instar larvae (p = 0.059). Our study demonstrated dramatic shifts in gut bacterial community structure between larvae and adults. Larvae fed on decaying wood and adults fed on beetle jelly, suggesting that diet is a crucial factor shaping the gut bacterial community structure. There were significant differences in bacterial community structure between early instar and final instars larvae, suggesting that certain life stages are associated with a defined gut bacterial community. [ABSTRACT FROM AUTHOR]

Simple Summary: Intestinal bacterial taxa play an important role in maintaining the normal physiological ecology of animals. Many factors affect the composition and diversity of the intestinal bacterial community, including diet, environment and season. However, the unique life cycle of birds makes it interesting to study their gut bacteria, especially migratory birds. Birds use many habitats and food resources, which may influence their intestinal bacterial community structure during seasonal migration. Hooded crane (Grus monacha) is one such migrant waterbird that traverses long distances and occupies varied habitats. In this study, we investigated the diversity and differences in intestinal bacterial communities of hooded cranes over the migratory season. The intestinal bacterial alpha-diversity of hooded cranes in winter was significantly higher than fall and spring. The gut bacterial community composition differed significantly across the three seasons (ANOSIM, P = 0.001). This study provides baseline information on the seasonal dynamics of intestinal bacteria in migratory hooded cranes. Intestinal bacterial communities form an integral component of the organism. Many factors influence gut bacterial community composition and diversity, including diet, environment and seasonality. During seasonal migration, birds use many habitats and food resources, which may influence their intestinal bacterial community structure. Hooded crane (Grus monacha) is a migrant waterbird that traverses long distances and occupies varied habitats. In this study, we investigated the diversity and differences in intestinal bacterial communities of hooded cranes over the migratory seasons. Fecal samples from hooded cranes were collected at a stopover site in two seasons (spring and fall) in Lindian, China, and at a wintering ground in Shengjin Lake, China. We analyzed bacterial communities from the fecal samples using high throughput sequencing (Illumina Mi-seq). Firmicutes, Proteobacteria, Tenericutes, Cyanobacteria, and Actinobacteria were the dominant phyla across all samples. The intestinal bacterial alpha-diversity of hooded cranes in winter was significantly higher than in fall and spring. The bacterial community composition significantly differed across the three seasons (ANOSIM, P = 0.001), suggesting that seasonal fluctuations may regulate the gut bacterial community composition of migratory birds. This study provides baseline information on the seasonal dynamics of intestinal bacterial community structure in migratory hooded cranes. [ABSTRACT FROM AUTHOR]

Adequate exploitation of legume–rhizobia symbiosis for nitrogen fixation may help to alleviate the overuse of chemical nitrogen fertilizer and aid in sustainable agricultural development. However, controlling this beneficial interaction requires thorough characterization of the effects of soil rhizosphere microorganisms, especially core taxa, on the legume–rhizobia symbiosis. Here, we used Illumina sequencing to investigate the effects of cover crop (Raphanus sativus L. and Lolium perenne L.) residue on the rhizosphere soil microbial community and peanut nodulation ability. The results indicated that Raphanus sativus L. amendment (RS) significantly increased soil available phosphorus (AP) content and peanut nodulation ability, while the Lolium perenne L. amendment (LP) had no noticeable impact on peanut nodulation. LP and RS significantly elevated bacterial and rhizobial diversity, reduced fungal diversity, and shifted microbial community structure (bacteria, 14.7%, p = 0.001; rhizobia, 21.7%, p = 0.001; fungi, 25.5%, p = 0.001). Random forest analysis found that the core rhizosphere taxa, sharing similar ecological preferences, were the primary drivers of peanut nodulation. By least squares regression, soil AP content was found to be positively correlated with the relative abundance of key ecological clusters. Furthermore, RS was found to promote peanut nodulation by increasing the relative abundance of critical rhizosphere taxa. Overall, our findings emphasize that core microbial taxa might play an essential function in the modulation of legume nodulation and provide scientific evidence for the effective management of the plant microbiome. [ABSTRACT FROM AUTHOR]

Simple Summary: The gut microbiome is expected to adapt to the varying energetic and nutritional pressures in females of different reproductive states. Although the genus Macaca has the widest geographical range of nonhuman primates, few empirical studies are currently available that explore the relationship between female reproductive states and their gut microbiome in this genus. We have examined variation of gut bacterial microbiome in free-ranging female Tibetan macaques (Macaca thibetana) across different reproductive states (cycling, pregnancy and lactation). We found significant changes in gut bacterial taxonomic composition, structure and their potential functions in different reproductive states of our study species. In particular, the relative abundance of Proteobacteria increased significantly during pregnancy and lactation. In addition, the relative abundance of Succinivibrionaceae and Succinivibrio (Succinivibrionaceae) were overrepresented in pregnant females, whereas Bifidobacteriaceae and Bifidobacterium (Bifidobacteriaceae) were overrepresented in lactating females. Furthermore, predicted functional genes of several metabolic pathways related to host's energy and nutrition, such as metabolism of carbohydrates, cofactors and vitamins, glycans and other amino acids, were overrepresented in pregnancy and lactation. Thus, our results suggest that the gut microbiome may play an important role in the energetic and nutritional strategies of female reproductive ecology in the genus Macaca. Future studies of the "microbial reproductive ecology" of primates that incorporate food availability, reproductive seasonality, female reproductive physiology and gut inflammation are warranted. The gut microbiome is expected to adapt to the varying energetic and nutritional pressures in females of different reproductive states. Changes in the gut microbiome may lead to varying nutrient utilizing efficiency in pregnant and lactating female primates. In this study, we examined variation in the gut bacterial community composition of wild female Tibetan macaques (Macaca thibetana) across different reproductive states (cycling, pregnancy and lactation). Fecal samples (n = 25) were collected from ten adult females harvested across different reproductive states. Gut microbial community composition and potential functions were assessed using 16 S rRNA gene sequences. We found significant changes in gut bacterial taxonomic composition, structure and their potential functions in different reproductive states of our study species. In particular, the relative abundance of Proteobacteria increased significantly during pregnancy and lactation. In addition, the relative abundance of Succinivibrionaceae and Succinivibrio (Succinivibrionaceae) were overrepresented in pregnant females, whereas Bifidobacteriaceae and Bifidobacterium (Bifidobacteriaceae) were overrepresented in lactating females. Furthermore, the relative abundance of predicted functional genes of several metabolic pathways related to host's energy and nutrition, such as metabolism of carbohydrates, cofactors and vitamins, glycans and other amino acids, were enriched in pregnancy and lactation. Our findings suggest that changes in the gut microbiome may play an important role in meeting the energetic needs of pregnant and lactating Tibetan macaques. Future studies of the "microbial reproductive ecology" of primates that incorporate food availability, reproductive seasonality, female reproductive physiology and gut inflammation are warranted. [ABSTRACT FROM AUTHOR]

Simple Summary: Intestinal microbiota play crucial roles for their hosts. Odontolabis fallaciosa shows striking sexual dimorphism and male trimorphism, which represents an interesting system to study their gut microbiota. We have compared the intestinal bacterial community structure between the two sexes and among three male morphs of O. fallaciosa. The gut bacterial community structure was significantly different between males and females. The females were associated with higher bacterial alpha-diversity relative to males. Large males had a higher relative abundance of Firmicutes and Firmicutes/Bacteroides (F/B) ratio, which contributed to nutritional efficiency. The results increased our understanding of beetle–bacterial interactions of O. fallaciosa between the two sexes, and among three male morphs, which might reveal the relationship among the gut microbiota, nutrition level, and phenotypic evolution of the stag beetle. Odontolabis fallaciosa (Coleoptera: Lucanidae) is a giant and popular stag beetle with striking sexual dimorphism and male trimorphism. However, little is known about their intestinal microbiota, which might play an indispensable role in shaping the health of their hosts. The aim of this study was to investigate the intestinal bacterial community structure between the two sexes and among three male morphs of O. fallaciosa from China using high-throughput sequencing (Illumina MiSeq). The gut bacterial community structure was significantly different between males and females, suggesting that sex appeared to be the crucial factor shaping the intestinal bacterial community. Females had higher bacterial alpha-diversity than males. There was little difference in gut bacterial community structure among the three male morphs. However, compared to medium and small males, large individuals were associated with the higher relative abundance of Firmicutes and Firmicutes/Bacteroides (F/B) ratio, which might contribute to nutritional efficiency. Overall, these results might help to further our understanding of beetle–bacterial interactions of O. fallaciosa between the two sexes, and among the three male morphs. [ABSTRACT FROM AUTHOR]