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David A. Relman - One of the best experts on this subject based on the ideXlab platform.

  • Marine mammals harbor unique Microbiotas shaped by and yet distinct from the sea
    Nature Communications, 2016
    Co-Authors: Elizabeth K. Costello, Alexandra D. Switzer, Benjamin J. Callahan, Susan P. Holmes, Randall S. Wells, Kevin P. Carlin, Eric D. Jensen, Stephanie Venn-watson, David A. Relman

    Marine mammals play crucial ecological roles in the oceans, but little is known about their Microbiotas. Here we study the bacterial communities in 337 samples from 5 body sites in 48 healthy dolphins and 18 healthy sea lions, as well as those of adjacent seawater and other hosts. The bacterial taxonomic compositions are distinct from those of other mammals, dietary fish and seawater, are highly diverse and vary according to body site and host species. Dolphins harbour 30 bacterial phyla, with 25 of them in the mouth, several abundant but poorly characterized Tenericutes species in gastric fluid and a surprisingly paucity of Bacteroidetes in distal gut. About 70% of near-full length bacterial 16S ribosomal RNA sequences from dolphins are unique. Host habitat, diet and phylogeny all contribute to variation in marine mammal distal gut Microbiota composition. Our findings help elucidate the factors structuring marine mammal Microbiotas and may enhance monitoring of marine mammal health. Little is known about the Microbiota of marine mammals, despite the crucial ecological roles played by these animals. Here, Bik et al . describe the bacterial communities associated with various body sites in dolphins and sea lions, as well as the Microbiota of their dietary fish and adjacent seawater.

Matteo Montagna - One of the best experts on this subject based on the ideXlab platform.

  • evidence for a conserved Microbiota across the different developmental stages of plodia interpunctella
    Insect Science, 2019
    Co-Authors: Valeria Mereghetti, D.p. Locatelli, L. Limonta, Bessem Chouaia, Matteo Montagna

    Diversity and composition of lepidopteran Microbiotas are poorly investigated, especially across the different developmental stages. To improve this knowledge, we characterize the Microbiota among different developmental stages of the Indian meal moth, Plodia interpunctella, which is considered one of the major pest of commodities worldwide. Using culture-independent approach based on Illumina 16S rRNA gene sequencing we characterized the Microbiota of four developmental stages: eggs, first and last instar larvae and adult. A total of 1022 bacterial OTUs were obtained, showing a quite diversified Microbiota associated to all the analyzed stages. The Microbiotas associated with P. interpunctella resulted almost constant throughout the developmental stages, with approximately 77% of bacterial OTUs belonging to the phylum of Proteobacteria. The dominant bacterial genus is represented by Burkholderia (∼64%), followed by Propionibacterium, Delftia, Pseudomonas and Stenotrophomonas. A core bacterial community, composed of 139 OTUs, were detected in all the developmental stages, among which 112 OTUs were assigned to the genus Burkholderia. A phylogenetic reconstruction, based on the 16S rRNA, revealed that our Burkholderia OTUs clustered with Burkholderia cepacia complex, in the same group of those isolated from the hemipterans Gossyparia spuria and Acanthococcus aceris. The functional profiling, predicted on the base of the bacterial 16S rRNA, indicates differences in the metabolic pathways related to metabolism of amino acids between preimaginal and adult stages. We can hypothesize that bacteria may support the insect host during preimaginal stages. This article is protected by copyright. All rights reserved

  • Evidence of a bacterial core in the stored products pest Plodia interpunctella: the influence of different diets
    Environmental Microbiology, 2016
    Co-Authors: Matteo Montagna, Valeria Mereghetti, Giorgio Gargari, Simone Guglielmetti, Franco Faoro, Giuseppe Carlo Lozzia, D.p. Locatelli, L. Limonta

    Summary The potential influence of insects' feeding behaviour on their associated bacterial communities is currently a matter of debate. Using the major pest of commodities, Plodia interpunctella, as a model and adopting a culture-independent approach, the impact of different diets on the host-associated Microbiota was evaluated. An analysis of similarity showed differences among the Microbiotas of moths fed with five substrates and provided evidence that diet represents the only tested factor that explains this dissimilarity. Bacteria shared between food and insects provide evidence for a limited conveyance to the host of the bacteria derived from the diet; more likely, the content of carbohydrates and proteins in the diets promotes changes in the insect's Microbiota. Moth Microbiotas were characterized by two robust entomotypes, respectively, associated with a carbohydrate-rich diet and a protein-rich diet. These results were also confirmed by the predicted metagenome functional potential. A core Microbiota, composed of six taxa, was shared between eggs and adults, regardless of the origin of the population. Finally, the identification of possible human and animal pathogens on chili and associated with the moths that feed on it highlights the possibility that these bacteria may be conveyed by moth frass.

Rob Knight - One of the best experts on this subject based on the ideXlab platform.

  • seasonal restructuring of the ground squirrel gut Microbiota over the annual hibernation cycle
    American Journal of Physiology-regulatory Integrative and Comparative Physiology, 2013
    Co-Authors: Hannah V Carey, William A Walters, Rob Knight

    Many hibernating mammals suspend food intake during winter, relying solely on stored lipids to fuel metabolism. Winter fasting in these species eliminates a major source of degradable substrates to support growth of gut microbes, which may affect microbial community structure and host-microbial interactions. We explored the effect of the annual hibernation cycle on gut Microbiotas using deep sequencing of 16S rRNA genes from ground squirrel cecal contents. Squirrel Microbiotas were dominated by members of the phyla Bacteroidetes, Firmicutes, and Verrucomicrobia. UniFrac analysis showed that Microbiotas clustered strongly by season, and maternal influences, diet history, host age, and host body temperature had minimal effects. Phylogenetic diversity and numbers of operational taxonomic units were lowest in late winter and highest in the spring after a 2-wk period of refeeding. Hibernation increased relative abundance of Bacteroidetes and Verrucomicrobia, phyla that contain species capable of surviving on host-derived substrates such as mucins, and reduced relative abundance of Firmicutes, many of which prefer dietary polysaccharides. Hibernation reduced cecal short-chain fatty acid and ammonia concentrations, and increased and decreased concentrations of acetate and butyrate, respectively. These results indicate that the ground squirrel Microbiota is restructured each year in a manner that reflects differences in microbial preferences for dietary vs. host-derived substrates, and thus the competitive abilities of different taxa to survive in the altered environment in the hibernator gut.

  • host remodeling of the gut microbiome and metabolic changes during pregnancy
    Cell, 2012
    Co-Authors: Omry Koren, Julia K Goodrich, Tyler C Cullender, Ayme Spor, Kirsi Laitinen, Helene Kling Backhed, Antonio Gonzalez, Jeffrey J Werner, Largus T Angenent, Rob Knight

    Summary Many of the immune and metabolic changes occurring during normal pregnancy also describe metabolic syndrome. Gut Microbiota can cause symptoms of metabolic syndrome in nonpregnant hosts. Here, to explore their role in pregnancy, we characterized fecal bacteria of 91 pregnant women of varying prepregnancy BMIs and gestational diabetes status and their infants. Similarities between infant-mother Microbiotas increased with children's age, and the infant Microbiota was unaffected by mother's health status. Gut Microbiota changed dramatically from first (T1) to third (T3) trimesters, with vast expansion of diversity between mothers, an overall increase in Proteobacteria and Actinobacteria, and reduced richness. T3 stool showed strongest signs of inflammation and energy loss; however, microbiome gene repertoires were constant between trimesters. When transferred to germ-free mice, T3 Microbiota induced greater adiposity and insulin insensitivity compared to T1. Our findings indicate that host-microbial interactions that impact host metabolism can occur and may be beneficial in pregnancy.

  • worlds within worlds evolution of the vertebrate gut Microbiota
    Nature Reviews Microbiology, 2008
    Co-Authors: Rob Knight, Catherine A Lozupone, Micah Hamady, Jeffrey I Gordon

    In this Analysis we use published 16S ribosomal RNA gene sequences to compare the bacterial assemblages that are associated with humans and other mammals, metazoa and free-living microbial communities that span a range of environments. The composition of the vertebrate gut Microbiota is influenced by diet, host morphology and phylogeny, and in this respect the human gut bacterial community is typical of an omnivorous primate. However, the vertebrate gut Microbiota is different from free-living communities that are not associated with animal body habitats. We propose that the recently initiated international Human Microbiome Project should strive to include a broad representation of humans, as well as other mammalian and environmental samples, as comparative analyses of Microbiotas and their microbiomes are a powerful way to explore the evolutionary history of the biosphere.

N. Principi - One of the best experts on this subject based on the ideXlab platform.

  • Impact of nasopharyngeal Microbiota on the development of respiratory tract diseases
    European Journal of Clinical Microbiology & Infectious Diseases, 2018
    Co-Authors: S. Esposito, N. Principi

    Knowledge of whether and how respiratory Microbiota composition can prime the immune system and provide colonisation resistance, limiting consecutive pathobiont overgrowth and infections, is essential to improving the prevention and therapy of respiratory disorders. Modulation of dysbiotic ecosystems or reconstitution of missing microbes might be a possible measure to reduce respiratory diseases. The aim of this review is to analyse the role of nasopharyngeal Microbiota in the development of respiratory tract disease in paediatric-age subjects. PubMed was used to search for all studies published over the last 15 years using the following key words: “Microbiota” or “microbioma” and “nasopharyngeal” or “respiratory” or “nasal” and “children” or “paediatric” or “infant”. Analysis of the literature showed that respiratory Microbiota can regulate health and disease development in the respiratory tract. Like the gut Microbiota, the respiratory Microbiota is established at birth, and early respiratory Microbiota composition determines bacterial succession patterns and respiratory health in children. Protective and dangerous bacteria have been identified, and this can be considered the base for developing new approaches to diseases that respond poorly to traditional interventions. Reconstitution of missing microbes can be achieved by the administration of pre- and probiotics. Modulation of respiratory Microbiota by favouring colonisation of the upper respiratory tract by beneficial commensals can interfere with the proliferation and activity of resident pathobionts and is a possible new measure to reduce the risk of disease. However, further studies are needed because a deeper understanding of these and related issues can be transferred to clinical practice.

Edouard Timsit - One of the best experts on this subject based on the ideXlab platform.

  • Topography of the respiratory tract bacterial Microbiota in cattle
    Microbiome, 2020
    Co-Authors: Christopher Mcmullen, Trevor W. Alexander, Renaud Léguillette, Matthew Workentine, Edouard Timsit

    Background Bacterial bronchopneumonia (BP) is the leading cause of morbidity and mortality in cattle. The nasopharynx is generally accepted as the primary source of pathogenic bacteria that cause BP. However, it has recently been shown in humans that the oropharynx may act as the primary reservoir for pathogens that reach the lung. The objective was therefore to describe the bacterial Microbiota present along the entire cattle respiratory tract to determine which upper respiratory tract (URT) niches may contribute the most to the composition of the lung Microbiota. Methods Seventeen upper and lower respiratory tract locations were sampled from 15 healthy feedlot steer calves. Samples were collected using a combination of swabs, protected specimen brushes, and saline washes. DNA was extracted from each sample and the 16S rRNA gene (V3-V4) was sequenced. Community composition, alpha-diversity, and beta-diversity were compared among sampling locations. Results Microbiota composition differed across sampling locations, with physiologically and anatomically distinct locations showing different relative abundances of 1137 observed sequence variants (SVs). An analysis of similarities showed that the lung was more similar to the nasopharynx (R-statistic = 0.091) than it was to the oropharynx (R-statistic = 0.709) or any other URT sampling location. Five distinct metacommunities were identified across all samples after clustering at the genus level using Dirichlet multinomial mixtures. This included a metacommunity found primarily in the lung and nasopharynx that was dominated by Mycoplasma . Further clustering at the SV level showed a shared metacommunity between the lung and nasopharynx that was dominated by Mycoplasma dispar . Other metacommunities found in the nostrils, tonsils, and oral Microbiotas were dominated by Moraxella , Fusobacterium , and Streptococcus , respectively. Conclusions The nasopharyngeal bacterial Microbiota is most similar to the lung bacterial Microbiota in healthy cattle and therefore may serve as the primary source of bacteria to the lung. This finding indicates that the nasopharynx is likely the most important location that should be targeted when doing bovine respiratory Microbiota research. Video abstract.