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      Egyptian Mongoose ( Herpestes ichneumon) Gut Microbiota: Taxonomical and Functional Differences across Sex and Age Classes

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          Abstract

          The Egyptian mongoose ( Herpestes ichneumon) is a medium-size carnivore that, in Europe, is restricted to Iberia. The bio-ecology of this species remains to be elucidated in several dimensions, including gut microbiota that is nowadays recognized as a fundamental component of mammals. In this work, we investigated the gut microbiota of this herpestid by single-molecule real-time sequencing of twenty paired male ( n = 10) and female ( n = 10) intestinal samples. This culture-independent approach enabled microbial profiling based on 16S rDNA and investigation of taxonomical and functional features. The core gut microbiome of the adult subpopulation was dominated by Firmicutes, Fusobacteria, Actinobacteria, and Proteobacteria. Eight genera were uniquely found in adults and five in non-adults. When comparing gut bacterial communities across sex, four genera were exclusive of females and six uniquely found in males. Despite these compositional distinctions, alpha- and beta-diversity analyses showed no statistically significant differences across sex or between adult and non-adult specimens. However, when function was inferred, males presented a significantly higher abundance of amino acid and citrate cycle metabolic pathways, compared to the significant overrepresentation in females of galactose metabolic pathways. Additionally, adults exhibited a significantly higher abundance of cationic antimicrobial peptide resistance pathways, while non-adults bared a significant overrepresentation of two-component systems associated with antibiotic synthesis, flagellin and biofilm production, and chemotaxis control. This study adds new insights into the mongoose bio-ecology palette, highlighting taxonomical and functional microbiome dissimilarities across sex and age classes, possibly related to primary production resources and life-history traits that impact on behavior and diet.

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          Most cited references 59

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          Has the microbiota played a critical role in the evolution of the adaptive immune system?

           Y Lee,  S. Mazmanian (2010)
          Although microbes have been classically viewed as pathogens, it is now well established that the majority of host-bacterial interactions are symbiotic. During development and into adulthood, gut bacteria shape the tissues, cells, and molecular profile of our gastrointestinal immune system. This partnership, forged over many millennia of coevolution, is based on a molecular exchange involving bacterial signals that are recognized by host receptors to mediate beneficial outcomes for both microbes and humans. We explore how specific aspects of the adaptive immune system are influenced by intestinal commensal bacteria. Understanding the molecular mechanisms that mediate symbiosis between commensal bacteria and humans may redefine how we view the evolution of adaptive immunity and consequently how we approach the treatment of numerous immunologic disorders.
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            The rebirth of culture in microbiology through the example of culturomics to study human gut microbiota.

            Bacterial culture was the first method used to describe the human microbiota, but this method is considered outdated by many researchers. Metagenomics studies have since been applied to clinical microbiology; however, a "dark matter" of prokaryotes, which corresponds to a hole in our knowledge and includes minority bacterial populations, is not elucidated by these studies. By replicating the natural environment, environmental microbiologists were the first to reduce the "great plate count anomaly," which corresponds to the difference between microscopic and culture counts. The revolution in bacterial identification also allowed rapid progress. 16S rRNA bacterial identification allowed the accurate identification of new species. Mass spectrometry allowed the high-throughput identification of rare species and the detection of new species. By using these methods and by increasing the number of culture conditions, culturomics allowed the extension of the known human gut repertoire to levels equivalent to those of pyrosequencing. Finally, taxonogenomics strategies became an emerging method for describing new species, associating the genome sequence of the bacteria systematically. We provide a comprehensive review on these topics, demonstrating that both empirical and hypothesis-driven approaches will enable a rapid increase in the identification of the human prokaryote repertoire.
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              Dominance and Diversity in Land Plant Communities: Numerical relations of species express the importance of competition in community function and evolution.

              Most plant communities consist of several or many species which compete for light, water, and nutrients. Species in a given community may be ranked by their relative success in competition; productivity seems to be the best measure of their success or importance in the community. Curves of decreasing productivity connect the few most important species (the dominants) with a larger number of species of intermediate importance (whose number primarily determines the community's diversity or richness in species) and a smaller number of rare species. These curves are of varied forms and are believed to express different patterns of competition and niche differentiation in communities. It is probably true of plants, as of animals, that no two species in a stable community occupy the same niche. Evolution of niche differentiation makes possible the occurrence together of many plant species which are partial, rather than direct, competitors. Species tend to evolve also toward habitat differentiation, toward scattering of their centers of maximum population density in relation to environmental gradients, so that few species are competing with one another in their population centers. Evolution of both niche and habitat differentiation permits many species to exist together in communities as partial competitors, with distributions broadly and continuously overlapping, forming the landscape's many intergrading communities.
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                Author and article information

                Journal
                Microorganisms
                Microorganisms
                microorganisms
                Microorganisms
                MDPI
                2076-2607
                11 March 2020
                March 2020
                : 8
                : 3
                Affiliations
                [1 ]INIAV, IP- National Institute for Agrarian and Veterinary Research, 2780-157 Oeiras, Portugal; andre.c.pereira94@ 123456gmail.com
                [2 ]Centre for Ecology, Evolution and Environmental Changes (cE3c), Faculdade de Ciências da Universidade de Lisboa, 1749-016 Lisboa, Portugal
                [3 ]Biosystems & Integrative Sciences Institute (BioISI), Faculdade de Ciências da Universidade de Lisboa, 1749-016 Lisboa, Portugal
                [4 ]Departamento de Biologia & CESAM, Universidade de Aveiro, 3810-193 Aveiro, Portugal; victor.bandeira@ 123456ua.pt (V.B.);
                Author notes
                [* ]Correspondence: monica.cunha@ 123456iniav.pt ; Tel.: +351-214-403-500
                Article
                microorganisms-08-00392
                10.3390/microorganisms8030392
                7143146
                32168965
                © 2020 by the authors.

                Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license ( http://creativecommons.org/licenses/by/4.0/).

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