Background: The initial intestinal microbiota acquired from different sources has profound impacts on animal health and productivity. In modern poultry production practices, the source(s) of the establishing microbes ...Background: The initial intestinal microbiota acquired from different sources has profound impacts on animal health and productivity. In modern poultry production practices, the source(s) of the establishing microbes and their overall contribution during development of gastrointestinal tract communities are still unclear. Using fertilized eggs from two independent sources, we assessed the impact of eggshell-and environmental-associated microbial communities on the successional processes and bacterial community structure throughout the intestinal tract of chickens for up to 6 weeks post-hatch.Results: Culturing and sequencing techniques identified a viable, highly diverse population of anaerobic bacteria on the eggshell. The jejunal, ileal, and cecal microbial communities for the egg-only, environment-only, and conventionally raised birds generally displayed similar successional patterns characterized by increasing community richness and evenness over time, with strains of Enterococcus, Romboutsia, and unclassified Lachnospiraceae abundant for all three input groups in both trials. Bacterial community structures differed significantly based on trial and microbiota input with the exception of the egg-exposed and conventional birds in the jejunum at week 1 and the ileum at week 6. Cecal community structures were different based on trial and microbiota input source, and cecal short-chain fatty acid profiles at week 6 highlighted functional differences as well.Conclusion: We identified distinct intestinal microbial communities and differing cecal short-chain fatty acid profiles between birds exposed to the microbiota associated with either the eggshell or environment, and those of conventionally hatched birds. Our data suggest the eggshell plays an appreciable role in the development of the chicken intestinal microbiota, especially in the jejunum and ileum where the community structure of the eggshellonly birds was similar to the structure of conventionally hatched birds. Our data identify a complex interplay between the eggshell and environmental microbiota during establishment and succession within the chicken gut.Further studies should explore the ability of eggshell-and environment-derived microbes to shape the dynamics of succession and how these communities can be targeted through interventions to promote gut health and mitigate food-borne pathogen colonization in poultry.展开更多
The cryptic lifestyle of most fungi necessitates molecular identification of the guild in environmental studies.Over the past decades,rapid development and affordability of molecular tools have tremendously improved i...The cryptic lifestyle of most fungi necessitates molecular identification of the guild in environmental studies.Over the past decades,rapid development and affordability of molecular tools have tremendously improved insights of the fungal diversity in all ecosystems and habitats.Yet,in spite of the progress of molecular methods,knowledge about functional properties of the fungal taxa is vague and interpretation of environmental studies in an ecologically meaningful manner remains challenging.In order to facilitate functional assignments and ecological interpretation of environmental studies we introduce a user friendly traits and character database FungalTraits operating at genus and species hypothesis levels.Combining the information from previous efforts such as FUNGuild and FunFun together with involvement of expert knowledge,we reannotated 10,210 and 151 fungal and Stramenopila genera,respectively.This resulted in a stand-alone spreadsheet dataset covering 17 lifestyle related traits of fungal and Stramenopila genera,designed for rapid functional assignments of environmental stud-ies.In order to assign the trait states to fungal species hypotheses,the scientific community of experts manually categorised and assigned available trait information to 697,413 fungal ITS sequences.On the basis of those sequences we were able to summarise trait and host information into 92,623 fungal species hypotheses at 1%dissimilarity threshold.展开更多
Correction to:Fungal Diversity(2020)105:116 https://doi.org/10.1007/s13225-020-00466-2 There were errors in the name of author LászlóG.Nagy and in affiliation no.31 in the original publication.The original a...Correction to:Fungal Diversity(2020)105:116 https://doi.org/10.1007/s13225-020-00466-2 There were errors in the name of author LászlóG.Nagy and in affiliation no.31 in the original publication.The original article has been corrected.展开更多
基金supported by U.S. Department of Agriculture-Agricultural Research Service (USDA-ARS) funds。
文摘Background: The initial intestinal microbiota acquired from different sources has profound impacts on animal health and productivity. In modern poultry production practices, the source(s) of the establishing microbes and their overall contribution during development of gastrointestinal tract communities are still unclear. Using fertilized eggs from two independent sources, we assessed the impact of eggshell-and environmental-associated microbial communities on the successional processes and bacterial community structure throughout the intestinal tract of chickens for up to 6 weeks post-hatch.Results: Culturing and sequencing techniques identified a viable, highly diverse population of anaerobic bacteria on the eggshell. The jejunal, ileal, and cecal microbial communities for the egg-only, environment-only, and conventionally raised birds generally displayed similar successional patterns characterized by increasing community richness and evenness over time, with strains of Enterococcus, Romboutsia, and unclassified Lachnospiraceae abundant for all three input groups in both trials. Bacterial community structures differed significantly based on trial and microbiota input with the exception of the egg-exposed and conventional birds in the jejunum at week 1 and the ileum at week 6. Cecal community structures were different based on trial and microbiota input source, and cecal short-chain fatty acid profiles at week 6 highlighted functional differences as well.Conclusion: We identified distinct intestinal microbial communities and differing cecal short-chain fatty acid profiles between birds exposed to the microbiota associated with either the eggshell or environment, and those of conventionally hatched birds. Our data suggest the eggshell plays an appreciable role in the development of the chicken intestinal microbiota, especially in the jejunum and ileum where the community structure of the eggshellonly birds was similar to the structure of conventionally hatched birds. Our data identify a complex interplay between the eggshell and environmental microbiota during establishment and succession within the chicken gut.Further studies should explore the ability of eggshell-and environment-derived microbes to shape the dynamics of succession and how these communities can be targeted through interventions to promote gut health and mitigate food-borne pathogen colonization in poultry.
基金Estonian Science Foundation grants PSG136,PRG632,PUT1170the University of Tartu(PLTOM20903)the European Regional Development Fund(Centre of Excellence EcolChange).
文摘The cryptic lifestyle of most fungi necessitates molecular identification of the guild in environmental studies.Over the past decades,rapid development and affordability of molecular tools have tremendously improved insights of the fungal diversity in all ecosystems and habitats.Yet,in spite of the progress of molecular methods,knowledge about functional properties of the fungal taxa is vague and interpretation of environmental studies in an ecologically meaningful manner remains challenging.In order to facilitate functional assignments and ecological interpretation of environmental studies we introduce a user friendly traits and character database FungalTraits operating at genus and species hypothesis levels.Combining the information from previous efforts such as FUNGuild and FunFun together with involvement of expert knowledge,we reannotated 10,210 and 151 fungal and Stramenopila genera,respectively.This resulted in a stand-alone spreadsheet dataset covering 17 lifestyle related traits of fungal and Stramenopila genera,designed for rapid functional assignments of environmental stud-ies.In order to assign the trait states to fungal species hypotheses,the scientific community of experts manually categorised and assigned available trait information to 697,413 fungal ITS sequences.On the basis of those sequences we were able to summarise trait and host information into 92,623 fungal species hypotheses at 1%dissimilarity threshold.
文摘Correction to:Fungal Diversity(2020)105:116 https://doi.org/10.1007/s13225-020-00466-2 There were errors in the name of author LászlóG.Nagy and in affiliation no.31 in the original publication.The original article has been corrected.
