Animal microbiome最新文献

{"title":"Analysis of differences in the rumen microbiome and metabolic function in prepartum dairy cows with different body condition scores.","authors":"Dewei Du, Yanzhe Wang, Yongji Gao, Lei Feng, Ziye Zhang, Zhiyong Hu","doi":"10.1186/s42523-024-00324-5","DOIUrl":"10.1186/s42523-024-00324-5","url":null,"abstract":"<p><strong>Background: </strong>The rumen is a crucial digestive organ for dairy cows. The rumen microbiota assists in the digestion of plant feed through microbe-mediated fermentation, during which the plant feed is transformed into nutrients for the cow's use. Variations in the composition and function of the rumen microbiome affect the energy utilization efficiency of dairy cows, which is one of the reasons for the varying body condition scores (BCSs). This study focused on prepartum Holstein dairy cows to analyze differences in rumen microbiota and metabolites among cows with different BCSs. Twelve prepartum dairy cows were divided into two groups, low BCS (LBCS, BCS = 2.75, n = 6) and high BCS (HBCS, BCS = 3.5, n = 6), to explore differences in microbial composition and metabolites.</p><p><strong>Results: </strong>In the HBCS group, the genera within the phylum Firmicutes exhibited stronger correlations and greater abundances. Phyla such as Firmicutes, Patescibacteria, Acidobacteriota, Euryarchaeota, and Desulfobacterota, in addition to most of their constituent microbial groups, were significantly more abundant in the HBCS group than in the LBCS group. At the genus level, the abundances of Anaerovibrio, Veillonellaceae_UCG_001, Ruminococcus_gauvreauii_group, Blautia, Eubacterium, Prevotellaceae_YAB2003_group, Schwartzia, and Halomonas significantly increased in the HBCS group. The citrate cycle, involved in carbohydrate metabolism, exhibited a significant enrichment trend, with a notable increase in the abundance of its key substrate, citrate, in the HBCS group. This increase was significantly positively correlated with the differential bacterial genera.</p><p><strong>Conclusion: </strong>In this study, prepartum dairy cows with higher BCS exhibited greater abundance of Firmicutes. This study provides theoretical support for microbiological research on dairy cows with different BCSs and suggests that regulating the rumen microbiome could help maintain prepartum dairy cows within an optimal BCS range.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":"6 1","pages":"35"},"PeriodicalIF":4.9,"publicationDate":"2024-06-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11194928/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141447676","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Improvement of insulin sensitivity by dietary fiber consumption during late pregnant sows is associated with gut microbiota regulation of tryptophan metabolism.","authors":"Yang Li, Jiaqi He, Lijia Zhang, Haoyu Liu, Meng Cao, Yan Lin, Shengyu Xu, Lianqiang Che, Zhengfeng Fang, Bin Feng, Jian Li, Yong Zhuo, De Wu","doi":"10.1186/s42523-024-00323-6","DOIUrl":"10.1186/s42523-024-00323-6","url":null,"abstract":"<p><strong>Background: </strong>Dietary fiber (DF) consumption was reported to improve insulin sensitivity, change the tryptophan metabolism, and alter the gut microbiota. Herein, this study aimed to investigate the effects of DF consumption on insulin sensitivity, tryptophan metabolism, and gut microbiota composition in sows during late pregnancy, and explore the relationship between tryptophan metabolites and insulin sensitivity regulated by DF supplementation.</p><p><strong>Results: </strong>Twelve sows were randomly assigned to two dietary treatment groups (six/group): the low-fiber (LF) group, which was fed a basal diet, and the high-fiber (HF) group, which was fed the basal diet supplemented with 22.60 g/kg inulin and 181.60 g/kg cellulose. During late pregnancy, meal test, glucose tolerance test, and insulin challenge test were used to investigate the insulin sensitivity of sows, using the percutaneous brachiocephalic vein catheterization technique. High DF consumption resulted in improved insulin sensitivity, especially during the second and third trimesters, and promoted serotonin production from tryptophan. Additionally, plasma serotonin concentration was positively correlated with the insulin sensitivity index during late pregnancy. Moreover, DF consumption elevated fecal short-chain fatty acid (SCFA) concentrations, altered fecal microbial diversity, and increased the abundances of Rikenellaceae_RC9_gut_group, Alloprevotella, Parabacteroides, Roseburia, and Sphaerochaeta, which were positively correlated to plasma serotonin concentration.</p><p><strong>Conclusions: </strong>DF consumption improved insulin sensitivity during late pregnancy in sows, which improved microbial diversity in fecal samples and increased fecal SCFA concentrations, resulting in a positive correlation with plasma serotonin level.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":"6 1","pages":"34"},"PeriodicalIF":4.9,"publicationDate":"2024-06-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11191243/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141437883","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Modulation of gut microbiota composition due to early weaning stress induces depressive behavior during the juvenile period in mice.","authors":"Itsuka Kamimura, Eiji Miyauchi, Tadashi Takeuchi, Noriaki Tsuchiya, Kanami Tamura, Ayumi Uesugi, Hiroki Negishi, Takashi Taida, Tamotsu Kato, Masami Kawasumi, Miho Nagasawa, Kazutaka Mogi, Hiroshi Ohno, Takefumi Kikusui","doi":"10.1186/s42523-024-00322-7","DOIUrl":"10.1186/s42523-024-00322-7","url":null,"abstract":"<p><strong>Background: </strong>The gut microbiota plays an important role in the development of behavior and immunity in infants and juveniles. Early weaning (EW), a form of social stress in mice, leads to increased anxiety and an enhanced stress response in the hypothalamic-pituitary-adrenal axis during adulthood. Early life stress also modulates the immune system and increases vulnerability to infection. However, studies investigating the causal relationships among juvenile stress, microbiota changes, and immune and behavioral deficits are limited. Therefore, we hypothesized that EW alters gut microbiota composition and impairs the development of the nervous and immune systems.</p><p><strong>Results: </strong>EW mice moved longer distances in the marble-burying test and had longer immobility times in the tail suspension test than normal weaning (NW) mice. In parallel, the gut microbiome composition differed between NW and EW mice, and the abundance of Erysipelotrichacea in EW mice at 8 weeks of age was lower than that in NW mice. In an empirical study, germ-free mice colonized with the gut microbiota of EW mice (GF-EW mice) demonstrated higher depressive behavior than GF mice colonized with normal weaning microbiota (GF-NW mice). Immune cell profiles were also affected by the EW microbiota colonization; the number of CD4 + T cells in the spleen was reduced in GF-EW mice.</p><p><strong>Conclusion: </strong>Our results suggest that EW-induced alterations in the gut microbiota cause depressive behaviors and modulate the immune system.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":"6 1","pages":"33"},"PeriodicalIF":4.9,"publicationDate":"2024-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11188262/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141433480","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Do fish gut microbiotas vary across spatial scales? A case study of Diplodus vulgaris in the Mediterranean Sea.","authors":"Ginevra Lilli, Charlotte Sirot, Hayley Campbell, Fanny Hermand, Deirdre Brophy, Jean-François Flot, Conor T Graham, Isabelle F George","doi":"10.1186/s42523-024-00319-2","DOIUrl":"10.1186/s42523-024-00319-2","url":null,"abstract":"<p><strong>Background: </strong>Biogeography has been linked to differences in gut microbiota in several animals. However, the existence of such a relationship in fish is not clear yet. So far, it seems to depend on the fish species studied. However, most studies of fish gut microbiotas are based on single populations. In this study, we investigated the gut microbiota of fish from three wild populations of the two-banded sea bream Diplodus vulgaris (Geoffroy Saint-Hilaire, 1817) to determine whether its diversity, structure and potential functionality reflect the geographic origin of the fish, at large and small geographical scale. Additionally, we explored the host- and environmental-related factors explaining this relationship.</p><p><strong>Results: </strong>We showed that the taxonomy and potential functionality of the mucosa-associated gut microbiota of Diplodus vulgaris differ to varying degrees depending on the spatial scale considered. At large scale, we observed that both the taxonomical structure and the potential functionality of the fish microbiota differed significantly between populations. In contrast, the taxonomical diversity of the microbial community displayed a significant relationship with factors other than the geographic origin of the fish (i.e. sampling date). On the other hand, at small scale, the different composition and diversity of the microbiota differ according to the characteristics of the habitat occupied by the fish. Specifically, we identified the presence of Posidonia oceanica in the benthic habitat as predictor of both the microbiota composition and diversity. Lastly, we reported the enrichment of functions related to the metabolism of xenobiotics (i.e. drugs and 4-aminobenzoate) in a population and we indicated it as a potential target of future monitoring.</p><p><strong>Conclusions: </strong>With this study, we confirmed the importance of investigating the gut microbiota of wild fish species using multiple populations, taking into account the different habitats occupied by the individuals. Furthermore, we underscored the use of the biodegradation potential of the gut microbiota as an alternative means of monitoring emerging contaminants in Mediterranean fish.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":"6 1","pages":"32"},"PeriodicalIF":4.9,"publicationDate":"2024-06-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11177387/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141319144","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Insect live larvae as a new nutritional model in duck: effects on gut health.","authors":"Elena Colombino, Marta Gariglio, Ilaria Biasato, Ilario Ferrocino, Sara Pozzo, Emma Fragola, Elena Battisti, Stefania Zanet, Ezio Ferroglio, Maria Teresa Capucchio, Achille Schiavone","doi":"10.1186/s42523-024-00316-5","DOIUrl":"10.1186/s42523-024-00316-5","url":null,"abstract":"<p><strong>Background: </strong>This study aimed to evaluate the effects of Hermetia illucens (Black soldier fly-BSF) and Tenebrio molitor (Yellow mealworm-YMW) live larvae as a new nutritional model on duck's gut health, considering gut histomorphometry, mucin composition, cytokines transcription levels, and microbiota. A total of 126, 3-days-old, females Muscovy ducks were randomly allotted to three dietary treatments (6 replicates/treatment, 7 birds/pen): (i) C: basal diet; (ii) BSF: C + BSF live larvae; (iii) YMW: C + YMW live larvae. BSF and YMW live larvae were administered on top of the basal diet, based on the 5% of the expected daily feed intake. The live weight, average daily gain, average daily feed intake and feed conversion ratio were evaluated for the whole experimental period. On day 52, 12 ducks/treatment (2 birds/replicate) were slaughtered and samples of duodenum, jejunum, ileum, spleen, liver, thymus and bursa of Fabricius were collected for histomorphometry. Mucin composition was evaluated in the small intestine through histochemical staining while jejunal MUC-2 and cytokines transcription levels were evaluated by rt-qPCR. Cecal microbiota was also analyzed by means of 16 S rRNA gene sequencing.</p><p><strong>Results: </strong>Birds' growth performance and histomorphometry were not influenced by diet, with a proximo-distal decreasing gradient from duodenum to ileum (p < 0.001), respecting the physiological gut development. Mucin staining intensity and MUC-2 gene expression did not vary among dietary treatments, even though mucin intensity increased from duodenum to ileum, according to normal gut mucus physiology (p < 0.001). Regarding local immune response, IL-6 was higher in YMW group when compared to the other groups (p = 0.009). Insect live larvae did not affect cecal microbiota diversity, but BSF and YMW groups showed a higher presence of Helicobacter, Elusimicrobium, and Succinatimonas and a lower abundance of Coriobacteriaceae and Phascolarctobacterium compared to C birds (p < 0.05).</p><p><strong>Conclusions: </strong>The use of BSF and YMW live larvae as new nutritional model did not impair gut development and mucin composition of Muscovy ducks, but slightly improved the intestinal immune status and the microbiota composition by enhancing regulatory cytokine IL-6 and by increasing minor Operational Taxonomic Units (OTUs) involved in short-chain fatty acids production.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":"6 1","pages":"31"},"PeriodicalIF":0.0,"publicationDate":"2024-05-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11137933/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141174147","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Integrating uterine microbiome and metabolome to advance the understanding of the uterine environment in dairy cows with metritis.","authors":"S Casaro, J G Prim, T D Gonzalez, F Cunha, R S Bisinotto, R C Chebel, J E P Santos, C D Nelson, S J Jeon, R C Bicalho, J P Driver, Klibs N Galvão","doi":"10.1186/s42523-024-00314-7","DOIUrl":"10.1186/s42523-024-00314-7","url":null,"abstract":"<p><strong>Background: </strong>Metritis is a prevalent uterine disease that affects the welfare, fertility, and survival of dairy cows. The uterine microbiome from cows that develop metritis and those that remain healthy do not differ from calving until 2 days postpartum, after which there is a dysbiosis of the uterine microbiome characterized by a shift towards opportunistic pathogens such as Fusobacteriota and Bacteroidota. Whether these opportunistic pathogens proliferate and overtake the uterine commensals could be determined by the type of substrates present in the uterus. The objective of this study was to integrate uterine microbiome and metabolome data to advance the understanding of the uterine environment in dairy cows that develop metritis. Holstein cows (n = 104) had uterine fluid collected at calving and at the day of metritis diagnosis. Cows with metritis (n = 52) were paired with cows without metritis (n = 52) based on days after calving. First, the uterine microbiome and metabolome were evaluated individually, and then integrated using network analyses.</p><p><strong>Results: </strong>The uterine microbiome did not differ at calving but differed on the day of metritis diagnosis between cows with and without metritis. The uterine metabolome differed both at calving and on the day of metritis diagnosis between cows that did and did not develop metritis. Omics integration was performed between 6 significant bacteria genera and 153 significant metabolites on the day of metritis diagnosis. Integration was not performed at calving because there were no significant differences in the uterine microbiome. A total of 3 bacteria genera (i.e. Fusobacterium, Porphyromonas, and Bacteroides) were strongly correlated with 49 metabolites on the day of metritis diagnosis. Seven of the significant metabolites at calving were among the 49 metabolites strongly correlated with opportunistic pathogenic bacteria on the day of metritis diagnosis. The main metabolites have been associated with attenuation of biofilm formation by commensal bacteria, opportunistic pathogenic bacteria overgrowth, tissue damage and inflammation, immune evasion, and immune dysregulation.</p><p><strong>Conclusions: </strong>The data integration presented herein helps advance the understanding of the uterine environment in dairy cows with metritis. The identified metabolites may provide a competitive advantage to the main uterine pathogens Fusobacterium, Porphyromonas and Bacteroides, and may be promising targets for future interventions aiming to reduce opportunistic pathogenic bacteria growth in the uterus.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":"6 1","pages":"30"},"PeriodicalIF":0.0,"publicationDate":"2024-05-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11131188/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141158971","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Microbial dynamics and vertical transmission of Escherichia coli across consecutive life stages of the black soldier fly (Hermetia illucens).","authors":"Noor Van Looveren, Freek IJdema, Niels van der Heijden, Mik Van Der Borght, Dries Vandeweyer","doi":"10.1186/s42523-024-00317-4","DOIUrl":"10.1186/s42523-024-00317-4","url":null,"abstract":"<p><strong>Background: </strong>The black soldier fly (BSF, Hermetia illucens L.) is one of the most promising insects for bioconversion of organic waste, which often carry a high microbial load with potential foodborne pathogens. Although horizontal transmission (from rearing substrate to larvae) has been extensively studied, less is known about vertical transmission of microorganisms, and particularly of foodborne pathogens, across different BSF life stages.</p><p><strong>Results: </strong>This study investigated the microbial dynamics and vertical transmission of Escherichia coli across different life stages (larvae, prepupae, pupae and adults) of one BSF life cycle and its associated substrate (chicken feed) and frass, based on a combination of general microbial counts (based on culture-dependent techniques) and the bacterial community composition (based on 16S rRNA gene sequencing). Multiple interactions between the microbiota of the substrate, frass and BSF larvae were affirmed. The larvae showed relative consistency among both the microbial counts and bacterial community composition. Diversification of the bacterial communities started during the pupal stage, while most notable changes of the microbial counts and bacterial community compositions occurred during metamorphosis to adults. Furthermore, vertical transmission of E. coli was investigated after substrate inoculation with approximately 7.0 log cfu/g of kanamycin-resistant E. coli, and monitoring E. coli counts from larval to adult stage. Although the frass still contained substantial levels of E. coli (> 4.5 log cfu/g) and E. coli was taken up by the larvae, limited vertical transmission of E. coli was observed with a decreasing trend until the prepupal stage. E. coli counts were below the detection limit (1.0 log cfu/g) for all BSF samples from the end of the pupal stage and the adult stage. Additionally, substrate inoculation of E. coli did not have a substantial impact on the bacterial community composition of the substrate, frass or different BSF life stages.</p><p><strong>Conclusions: </strong>The fluctuating microbial counts and bacterial community composition underscored the dynamic character of the microbiota of BSF life stages. Additionally, vertical transmission throughout one BSF life cycle was not observed for E. coli. Hence, these findings paved the way for future case studies on vertical transmission of foodborne pathogens across consecutive BSF life stages or other insect species.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":"6 1","pages":"29"},"PeriodicalIF":0.0,"publicationDate":"2024-05-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11129375/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141154432","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Early-life factors shaping the gut microbiota of Common buzzard nestlings.","authors":"Hugo Pereira, Nayden Chakarov, Joseph I Hoffman, Tony Rinaud, Meinolf Ottensmann, Kai-Philipp Gladow, Busche Tobias, Barbara A Caspers, Öncü Maraci, Oliver Krüger","doi":"10.1186/s42523-024-00313-8","DOIUrl":"10.1186/s42523-024-00313-8","url":null,"abstract":"<p><strong>Background: </strong>Exploring the dynamics of gut microbiome colonisation during early-life stages is important for understanding the potential impact of microbes on host development and fitness. Evidence from model organisms suggests a crucial early-life phase when shifts in gut microbiota can lead to immune dysregulation and reduced host condition. However, our understanding of gut microbiota colonisation in long-lived vertebrates, especially during early development, remains limited. We therefore used a wild population of common buzzard nestlings (Buteo buteo) to investigate connections between the early-life gut microbiota colonisation, environmental and host factors.</p><p><strong>Results: </strong>We targeted both bacterial and eukaryotic microbiota using the 16S and 28S rRNA genes. We sampled the individuals during early developmental stages in a longitudinal design. Our data revealed that age significantly affected microbial diversity and composition. Nest environment was a notable predictor of microbiota composition, with particularly eukaryotic communities differing between habitats occupied by the hosts. Nestling condition and infection with the blood parasite Leucocytozoon predicted microbial community composition.</p><p><strong>Conclusion: </strong>Our findings emphasise the importance of studying microbiome dynamics to capture changes occurring during ontogeny. They highlight the role of microbial communities in reflecting host health and the importance of the nest environment for the developing nestling microbiome. Overall, this study contributes to understanding the complex interplay between microbial communities, host factors, and environmental variables, and sheds light on the ecological processes governing gut microbial colonisation during early-life stages.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":"6 1","pages":"27"},"PeriodicalIF":0.0,"publicationDate":"2024-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11092241/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140923582","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A taste of wilderness: supplementary feeding of red deer (Cervus elaphus) increases individual bacterial microbiota diversity but lowers abundance of important gut symbionts.","authors":"Luis Víquez-R, Maik Henrich, Vanessa Riegel, Marvin Bader, Kerstin Wilhelm, Marco Heurich, Simone Sommer","doi":"10.1186/s42523-024-00315-6","DOIUrl":"10.1186/s42523-024-00315-6","url":null,"abstract":"<p><p>The gut microbiome plays a crucial role in the health and well-being of animals. It is especially critical for ruminants that depend on this bacterial community for digesting their food. In this study, we investigated the effects of management conditions and supplemental feeding on the gut bacterial microbiota of red deer (Cervus elaphus) in the Bavarian Forest National Park, Germany. Fecal samples were collected from free-ranging deer, deer within winter enclosures, and deer in permanent enclosures. The samples were analyzed by high-throughput sequencing of the 16 S rRNA gene. The results showed that the gut bacterial microbiota differed in diversity, abundance, and heterogeneity within and between the various management groups. Free-ranging deer exhibited lower alpha diversity compared with deer in enclosures, probably because of the food supplementation available to the animals within the enclosures. Free-living individuals also showed the highest beta diversity, indicating greater variability in foraging grounds and plant species selection. Moreover, free-ranging deer had the lowest abundance of potentially pathogenic bacterial taxa, suggesting a healthier gut microbiome. Winter-gated deer, which spent some time in enclosures, exhibited intermediate characteristics between free-ranging and all-year-gated deer. These findings suggest that the winter enclosure management strategy, including supplementary feeding with processed plants and crops, has a significant impact on the gut microbiome composition of red deer. Overall, this study provides important insights into the effects of management conditions, particularly winter enclosure practices, on the gut microbiome of red deer. Understanding these effects is crucial for assessing the potential health implications of management strategies and highlights the value of microbiota investigations as health marker.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":"6 1","pages":"28"},"PeriodicalIF":0.0,"publicationDate":"2024-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11094858/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140923576","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Volatiles of symbiotic bacterial origin explain ectoparasitism and fledging success of hoopoes.","authors":"Mónica Mazorra-Alonso, Juan Manuel Peralta-Sánchez, Manuel Martín-Vivaldi, Manuel Martínez-Bueno, Rafael Núñez Gómez, Juan José Soler","doi":"10.1186/s42523-024-00312-9","DOIUrl":"10.1186/s42523-024-00312-9","url":null,"abstract":"<p><strong>Background: </strong>Some parasites use olfactory cues to detect their hosts and, since bacterial symbionts are partially responsible for animal odours, they could influence host parasitism. By autoclaving nest materials of hoopoe (Upupa epops) nests before reproduction started, we explored the hypothetical links between host-associated bacteria, volatiles and parasitism. During the nestling stage, we (i) estimated the level of ectoparasitism by chewing lice (Suborder Mallophaga) in adult hoopoe females and by Carnus haemapterus flies in nestlings, and (ii) characterized microbial communities and volatile profiles of nest environments (nest material and nest cavity, respectively) and uropygial secretions.</p><p><strong>Results: </strong>Experimental nests had less diverse bacterial communities and more diverse volatile profiles than control nests, while occupants experienced lower intensity of parasitism in experimental than in control nests. The experiment also affected beta diversity of the microbial communities of nest material and of the volatiles of the nestling uropygial secretions. Moreover, microbial communities of uropygial secretions and of nest materials covaried with their volatile profiles, while the volatile profile of the bird secretions explained nest volatile profile. Finally, a subset of the volatiles and bacteria detected in the nest material and uropygial secretions were associated with the ectoparasitism intensity of both adult females and nestlings, and with fledging success.</p><p><strong>Conclusions: </strong>These results show that a component of animal odours is linked with the microbial communities of the host and its reproductive environment, and emphasize that the associations between bacteria, ectoparasitism and reproductive success are partially mediated by volatiles of bacterial origin. Future work should focus on mechanisms underlying the detected patterns.</p>","PeriodicalId":72201,"journal":{"name":"Animal microbiome","volume":"6 1","pages":"26"},"PeriodicalIF":0.0,"publicationDate":"2024-05-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11084096/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140900652","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}