Wemheuer, Bernd

[["dc.bibliographiccitation.artnumber","S-895"],["dc.bibliographiccitation.firstpage","S-895"],["dc.bibliographiccitation.issue","6"],["dc.bibliographiccitation.journal","Gastroenterology"],["dc.bibliographiccitation.volume","156"],["dc.contributor.author","Coffey, Michael J."],["dc.contributor.author","Nielsen, Shaun"],["dc.contributor.author","Wemheuer, Bernd"],["dc.contributor.author","Garg, Millie"],["dc.contributor.author","Needham, Bronwen"],["dc.contributor.author","Jaffe, Adam"],["dc.contributor.author","Thomas, Torsten"],["dc.contributor.author","Ooi, Chee Y."],["dc.date.accessioned","2020-04-28T12:40:19Z"],["dc.date.available","2020-04-28T12:40:19Z"],["dc.date.issued","2019"],["dc.identifier.doi","10.1016/S0016-5085(19)39210-8"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/64439"],["dc.language.iso","en"],["dc.relation.issn","0016-5085"],["dc.title","Mo1947 – Taxonomic and Functional Intestinal Dysbiosis in Children with Cystic Fibrosis"],["dc.type","journal_article"],["dc.type.internalPublication","unknown"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","111"],["dc.bibliographiccitation.issue","1"],["dc.bibliographiccitation.journal","The Ocular Surface"],["dc.bibliographiccitation.lastpage","118"],["dc.bibliographiccitation.volume","17"],["dc.contributor.author","Ozkan, Jerome"],["dc.contributor.author","Willcox, Mark"],["dc.contributor.author","Wemheuer, Bernd"],["dc.contributor.author","Wilcsek, Geoff"],["dc.contributor.author","Coroneo, Minas"],["dc.contributor.author","Thomas, Torsten"],["dc.date.accessioned","2020-03-12T08:48:50Z"],["dc.date.available","2020-03-12T08:48:50Z"],["dc.date.issued","2019"],["dc.description.abstract","The human eye is composed of numerous microhabitats. The aim of this study was to understand the communality and differences in the microbiomes of various regions of the eye."],["dc.identifier.doi","10.1016/j.jtos.2018.11.005"],["dc.identifier.pmid","30445178"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/63322"],["dc.language.iso","en"],["dc.relation.eissn","1937-5913"],["dc.relation.issn","1542-0124"],["dc.title","Biogeography of the human ocular microbiota"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.artnumber","18593"],["dc.bibliographiccitation.issue","1"],["dc.bibliographiccitation.journal","Scientific Reports"],["dc.bibliographiccitation.volume","9"],["dc.contributor.author","Coffey, Michael J."],["dc.contributor.author","Nielsen, Shaun"],["dc.contributor.author","Wemheuer, Bernd"],["dc.contributor.author","Kaakoush, Nadeem O."],["dc.contributor.author","Garg, Millie"],["dc.contributor.author","Needham, Bronwen"],["dc.contributor.author","Pickford, Russell"],["dc.contributor.author","Jaffe, Adam"],["dc.contributor.author","Thomas, Torsten"],["dc.contributor.author","Ooi, Chee Y."],["dc.date.accessioned","2020-04-28T12:39:54Z"],["dc.date.available","2020-04-28T12:39:54Z"],["dc.date.issued","2019"],["dc.description.abstract","Intestinal dysbiosis has been observed in children with cystic fibrosis (CF), yet the functional consequences are poorly understood. We investigated the functional capacity of intestinal microbiota and inflammation in children with CF. Stool samples were collected from 27 children with CF and 27 age and gender matched healthy controls (HC) (aged 0.8-18 years). Microbial communities were investigated by iTag sequencing of 16S rRNA genes and functional profiles predicted using Tax4Fun. Inflammation was measured by faecal calprotectin and M2-pyruvate kinase. Paediatric CF gastrointestinal microbiota demonstrated lower richness and diversity compared to HC. CF samples exhibited a marked taxonomic and inferred functional dysbiosis when compared to HC. In children with CF, we predicted an enrichment of genes involved in short-chain fatty acid (SCFA), antioxidant and nutrient metabolism (relevant for growth and nutrition) in CF. The notion of pro-inflammatory GI microbiota in children with CF is supported by positive correlations between intestinal inflammatory markers and both genera and functional pathways. We also observed an association between intestinal genera and both growth z-scores and FEV1%. These taxonomic and functional changes provide insights into gastrointestinal disease in children with CF and future gastrointestinal therapeutics for CF should explore the aforementioned pathways and microbial changes."],["dc.identifier.doi","10.1038/s41598-019-55028-7"],["dc.identifier.pmid","31819107"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/64436"],["dc.language.iso","en"],["dc.relation.issn","2045-2322"],["dc.title","Gut Microbiota in Children With Cystic Fibrosis: A Taxonomic and Functional Dysbiosis"],["dc.type","journal_article"],["dc.type.internalPublication","no"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.issue","4"],["dc.bibliographiccitation.journal","mSystems"],["dc.bibliographiccitation.volume","4"],["dc.contributor.author","Zhang, Shan"],["dc.contributor.author","Song, Weizhi"],["dc.contributor.author","Wemheuer, Bernd"],["dc.contributor.author","Reveillaud, Julie"],["dc.contributor.author","Webster, Nicole"],["dc.contributor.author","Thomas, Torsten"],["dc.date.accessioned","2020-04-28T12:40:05Z"],["dc.date.available","2020-04-28T12:40:05Z"],["dc.date.issued","2019"],["dc.description.abstract","Thaumarchaeota are frequently reported to associate with marine sponges (phylum Porifera); however, little is known about the features that distinguish them from their free-living thaumarchaeal counterparts. In this study, thaumarchaeal metagenome-assembled genomes (MAGs) were reconstructed from metagenomic data sets derived from the marine sponges Hexadella detritifera, Hexadella cf. detritifera, and Stylissa flabelliformis Phylogenetic and taxonomic analyses revealed that the three thaumarchaeal MAGs represent two new species within the genus Nitrosopumilus and one novel genus, for which we propose the names \"CandidatusUNitrosopumilus hexadellus,\" \"CandidatusUNitrosopumilus detritiferus,\" and \"CandidatusUCenporiarchaeum stylissum\" (the U superscript indicates that the taxon is uncultured). Comparison of these genomes to data from the Sponge Earth Microbiome Project revealed that \"CaUCenporiarchaeum stylissum\" has been exclusively detected in sponges and can hence be classified as a specialist, while \"CaUNitrosopumilus detritiferus\" and \"CaUNitrosopumilus hexadellus\" are also detected outside the sponge holobiont and likely lead a generalist lifestyle. Comparison of the sponge-associated MAGs to genomes of free-living Thaumarchaeota revealed signatures that indicate functional features of a sponge-associated lifestyle, and these features were related to nutrient transport and metabolism, restriction-modification, defense mechanisms, and host interactions. Each species exhibited distinct functional traits, suggesting that they have reached different stages of evolutionary adaptation and/or occupy distinct ecological niches within their sponge hosts. Our study therefore offers new evolutionary and ecological insights into the symbiosis between sponges and their thaumarchaeal symbionts.IMPORTANCE Sponges represent ecologically important models to understand the evolution of symbiotic interactions of metazoans with microbial symbionts. Thaumarchaeota are commonly found in sponges, but their potential adaptations to a host-associated lifestyle are largely unknown. Here, we present three novel sponge-associated thaumarchaeal species and compare their genomic and predicted functional features with those of closely related free-living counterparts. We found different degrees of specialization of these thaumarchaeal species to the sponge environment that is reflected in their host distribution and their predicted molecular and metabolic properties. Our results indicate that Thaumarchaeota may have reached different stages of evolutionary adaptation in their symbiosis with sponges."],["dc.identifier.doi","10.1128/mSystems.00288-19"],["dc.identifier.pmid","31409660"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/64437"],["dc.language.iso","en"],["dc.relation.issn","2379-5077"],["dc.title","Comparative Genomics Reveals Ecological and Evolutionary Insights into Sponge-Associated Thaumarchaeota"],["dc.type","journal_article"],["dc.type.internalPublication","no"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","807"],["dc.bibliographiccitation.issue","3"],["dc.bibliographiccitation.journal","The ISME Journal"],["dc.bibliographiccitation.lastpage","817"],["dc.bibliographiccitation.volume","15"],["dc.contributor.author","Song, Weizhi"],["dc.contributor.author","Wemheuer, Bernd"],["dc.contributor.author","Steinberg, Peter D."],["dc.contributor.author","Marzinelli, Ezequiel M."],["dc.contributor.author","Thomas, Torsten"],["dc.date.accessioned","2021-04-14T08:28:40Z"],["dc.date.available","2021-04-14T08:28:40Z"],["dc.date.issued","2021"],["dc.identifier.doi","10.1038/s41396-020-00815-8"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/82675"],["dc.language.iso","en"],["dc.notes.intern","DOI Import GROB-399"],["dc.relation.eissn","1751-7370"],["dc.relation.issn","1751-7362"],["dc.title","Contribution of horizontal gene transfer to the functionality of microbial biofilm on a macroalgae"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","275"],["dc.bibliographiccitation.issue","2"],["dc.bibliographiccitation.journal","Microbial Biotechnology"],["dc.bibliographiccitation.lastpage","288"],["dc.bibliographiccitation.volume","12"],["dc.contributor.author","Wilkes Walburn, Jackson"],["dc.contributor.author","Wemheuer, Bernd"],["dc.contributor.author","Thomas, Torsten"],["dc.contributor.author","Copeland, Elizabeth"],["dc.contributor.author","O'Connor, Wayne"],["dc.contributor.author","Booth, Mark"],["dc.contributor.author","Fielder, Stewart"],["dc.contributor.author","Egan, Suhelen"],["dc.date.accessioned","2020-04-28T12:40:44Z"],["dc.date.available","2020-04-28T12:40:44Z"],["dc.date.issued","2019"],["dc.description.abstract","The supply of quality juveniles via land-based larviculture represents a major bottleneck to the growing finfish aquaculture industry. As the microbiome plays a key role in animal health, this study aimed to assess the microbial community associated with early larval development of commercially raised Yellowtail Kingfish (Seriola lalandi). We used qPCR and 16S rRNA gene amplicon sequencing to monitor changes in the microbiome associated with the development of S. lalandi from larvae to juveniles. We observed an increase in the bacterial load during larval development, which consisted of a small but abundant core microbiota including taxa belonging to the families Rhodobacteraceae, Lactobacillaceae and Vibrionaceae. The greatest change in the microbiome occurred as larvae moved from a diet of live feeds to formulated pellets, characterized by a transition from Proteobacteria to Firmicutes as the dominant phylum. A prediction of bacterial gene functions found lipid metabolism and secondary metabolite production were abundant in the early larval stages, with carbohydrate and thiamine metabolism functions increasing in abundance as the larvae age and are fed formulated diets. Together, these results suggest that diet is a major contributor to the early microbiome development of commercially raised S. lalandi."],["dc.identifier.doi","10.1111/1751-7915.13323"],["dc.identifier.pmid","30506824"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/64442"],["dc.language.iso","en"],["dc.relation.issn","1751-7915"],["dc.title","Diet and diet-associated bacteria shape early microbiome development in Yellowtail Kingfish (Seriola lalandi)"],["dc.type","journal_article"],["dc.type.internalPublication","no"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.artnumber","992"],["dc.bibliographiccitation.issue","1"],["dc.bibliographiccitation.journal","Nature Communications"],["dc.bibliographiccitation.volume","10"],["dc.contributor.author","Lurgi, Miguel"],["dc.contributor.author","Thomas, Torsten"],["dc.contributor.author","Wemheuer, Bernd"],["dc.contributor.author","Webster, Nicole S."],["dc.contributor.author","Montoya, Jose M."],["dc.date.accessioned","2020-03-12T08:39:30Z"],["dc.date.available","2020-03-12T08:39:30Z"],["dc.date.issued","2019"],["dc.description.abstract","Defining the organisation of species interaction networks and unveiling the processes behind their assembly is fundamental to understanding patterns of biodiversity, community stability and ecosystem functioning. Marine sponges host complex communities of microorganisms that contribute to their health and survival, yet the mechanisms behind microbiome assembly are largely unknown. We present the global marine sponge-microbiome network and reveal a modular organisation in both community structure and function. Modules are linked by a few sponge species that share microbes with other species around the world. Further, we provide evidence that abiotic factors influence the structuring of the sponge microbiome when considering all microbes present, but biotic interactions drive the assembly of more intimately associated 'core' microorganisms. These findings suggest that both ecological and evolutionary processes are at play in host-microbe network assembly. We expect mechanisms behind microbiome assembly to be consistent across multicellular hosts throughout the tree of life."],["dc.identifier.doi","10.1038/s41467-019-08925-4"],["dc.identifier.pmid","30824706"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/63319"],["dc.language.iso","en"],["dc.relation.eissn","2041-1723"],["dc.relation.issn","2041-1723"],["dc.title","Modularity and predicted functions of the global sponge-microbiome network"],["dc.type","journal_article"],["dc.type.internalPublication","no"],["dspace.entity.type","Publication"]]

[["dc.contributor.author","Wemheuer, Franziska"],["dc.contributor.author","Taylor, Jessica A."],["dc.contributor.author","Daniel, Rolf"],["dc.contributor.author","Johnston, Emma"],["dc.contributor.author","Meinicke, Peter"],["dc.contributor.author","Thomas, Torsten"],["dc.contributor.author","Wemheuer, Bernd"],["dc.date.accessioned","2020-04-28T12:40:33Z"],["dc.date.available","2020-04-28T12:40:33Z"],["dc.date.issued","2018"],["dc.description.abstract","Assessing the functional capability and redundancy of a microbial community is a major challenge in environmental microbiology. To address this challenge, we developed Tax4Fun2, a R-based tool for the rapid prediction of functional profiles and functional redundancy of prokaryotic communities from 16S rRNA gene sequences. By incorporating user-defined, habitat-specific genomic information, the accuracy and robustness of predicted functional profiles can be substantially enhanced."],["dc.format.extent","21"],["dc.identifier.doi","10.1101/490037"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/64441"],["dc.language.iso","en"],["dc.title","Tax4Fun2: a R-based tool for the rapid prediction of habitat-specific functional profiles and functional redundancy based on 16S rRNA gene marker gene sequences"],["dc.type","preprint"],["dc.type.internalPublication","yes"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","4268"],["dc.bibliographiccitation.issue","10"],["dc.bibliographiccitation.journal","Investigative Ophthalmology & Visual Science"],["dc.bibliographiccitation.lastpage","4276"],["dc.bibliographiccitation.volume","59"],["dc.contributor.author","Ozkan, Jerome"],["dc.contributor.author","Coroneo, Minas"],["dc.contributor.author","Willcox, Mark"],["dc.contributor.author","Wemheuer, Bernd"],["dc.contributor.author","Thomas, Torsten"],["dc.date.accessioned","2020-04-28T12:41:08Z"],["dc.date.available","2020-04-28T12:41:08Z"],["dc.date.issued","2018"],["dc.description.abstract","Knowledge of whether microorganisms reside in protected niches of the conjunctiva is potentially significant in terms of minimizing risks of contact lens inflammation/infection and endophthalmitis. We define if and how microbial communities from limbal and forniceal conjunctival tissue differ from those on the conjunctival surface."],["dc.identifier.doi","10.1167/iovs.18-24651"],["dc.identifier.pmid","30140925"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/64445"],["dc.language.iso","en"],["dc.relation.issn","1552-5783"],["dc.title","Identification and Visualization of a Distinct Microbiome in Ocular Surface Conjunctival Tissue"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dspace.entity.type","Publication"]]