当前期刊: Microbiome Go to current issue    加入关注    本刊投稿指南
显示样式:        排序: IF: - GO 导出
  • Correction to: The chemodiversity of paddy soil dissolved organic matter correlates with microbial community at continental scales
    Microbiome (IF 11.607) Pub Date : 2020-11-28
    Hong-Yi Li; Hang Wang; Hai-Tao Wang; Pei-Yong Xin; Xin-Hua Xu; Yun Ma; Wei-Ping Liu; Chang-Yun Teng; Cheng-Liang Jiang; Li-Ping Lou; Wyatt Arnold; Lauren Cralle; Yong-Guan Zhu; Jin-Fang Chu; Jack A. Gilbert; Zhi-Jian Zhang

    An amendment to this paper has been published and can be accessed via the original article.

  • Genetic selection for growth drives differences in intestinal microbiota composition and parasite disease resistance in gilthead sea bream
    Microbiome (IF 11.607) Pub Date : 2020-11-23
    M. Carla Piazzon; Fernando Naya-Català; Erick Perera; Oswaldo Palenzuela; Ariadna Sitjà-Bobadilla; Jaume Pérez-Sánchez

    The key effects of intestinal microbiota in animal health have led to an increasing interest in manipulating these bacterial populations to improve animal welfare. The aquaculture sector is no exception and in the last years, many studies have described these populations in different fish species. However, this is not an easy task, as intestinal microbiota is composed of very dynamic populations that

  • Perinatal environment shapes microbiota colonization and infant growth: impact on host response and intestinal function
    Microbiome (IF 11.607) Pub Date : 2020-11-23
    M. Selma-Royo; M. Calatayud Arroyo; I. García-Mantrana; A. Parra-Llorca; R. Escuriet; C. Martínez-Costa; M. C. Collado

    Early microbial colonization triggers processes that result in intestinal maturation and immune priming. Perinatal factors, especially those associated with birth, including both mode and place of delivery are critical to shaping the infant gut microbiota with potential health consequences. Gut microbiota profile of 180 healthy infants (n = 23 born at home and n = 157 born in hospital, 41.7% via cesarean

  • VALENCIA: a nearest centroid classification method for vaginal microbial communities based on composition
    Microbiome (IF 11.607) Pub Date : 2020-11-23
    Michael T. France; Bing Ma; Pawel Gajer; Sarah Brown; Michael S. Humphrys; Johanna B. Holm; L. Elaine Waetjen; Rebecca M. Brotman; Jacques Ravel

    Taxonomic profiles of vaginal microbial communities can be sorted into a discrete number of categories termed community state types (CSTs). This approach is advantageous because collapsing a hyper-dimensional taxonomic profile into a single categorical variable enables efforts such as data exploration, epidemiological studies, and statistical modeling. Vaginal communities are typically assigned to

  • Microbial function and genital inflammation in young South African women at high risk of HIV infection
    Microbiome (IF 11.607) Pub Date : 2020-11-21
    Arghavan Alisoltani; Monalisa T. Manhanzva; Matthys Potgieter; Christina Balle; Liam Bell; Elizabeth Ross; Arash Iranzadeh; Michelle du Plessis; Nina Radzey; Zac McDonald; Bridget Calder; Imane Allali; Nicola Mulder; Smritee Dabee; Shaun Barnabas; Hoyam Gamieldien; Adam Godzik; Jonathan M. Blackburn; David L. Tabb; Linda-Gail Bekker; Heather B. Jaspan; Jo-Ann S. Passmore; Lindi Masson

    Female genital tract (FGT) inflammation is an important risk factor for HIV acquisition. The FGT microbiome is closely associated with inflammatory profile; however, the relative importance of microbial activities has not been established. Since proteins are key elements representing actual microbial functions, this study utilized metaproteomics to evaluate the relationship between FGT microbial function

  • Antimicrobial use and production system shape the fecal, environmental, and slurry resistomes of pig farms
    Microbiome (IF 11.607) Pub Date : 2020-11-19
    Oscar Mencía-Ares; Raúl Cabrera-Rubio; José Francisco Cobo-Díaz; Avelino Álvarez-Ordóñez; Manuel Gómez-García; Héctor Puente; Paul D. Cotter; Fiona Crispie; Ana Carvajal; Pedro Rubio; Héctor Argüello

    The global threat of antimicrobial resistance (AMR) is a One Health problem impacted by antimicrobial use (AMU) for human and livestock applications. Extensive Iberian swine production is based on a more sustainable and eco-friendly management system, providing an excellent opportunity to evaluate how sustained differences in AMU impact the resistome, not only in the animals but also on the farm environment

  • New viral biogeochemical roles revealed through metagenomic analysis of Lake Baikal
    Microbiome (IF 11.607) Pub Date : 2020-11-19
    F. H. Coutinho; P. J. Cabello-Yeves; R. Gonzalez-Serrano; R. Rosselli; M. López-Pérez; T. I. Zemskaya; A. S. Zakharenko; V. G. Ivanov; F. Rodriguez-Valera

    Lake Baikal is the largest body of liquid freshwater on Earth. Previous studies have described the microbial composition of this habitat, but the viral communities from this ecosystem have not been characterized in detail. Here, we describe the viral diversity of this habitat across depth and seasonal gradients. We discovered 19,475 bona fide viral sequences, which are derived from viruses predicted

  • Characterization of TMAO productivity from carnitine challenge facilitates personalized nutrition and microbiome signatures discovery
    Microbiome (IF 11.607) Pub Date : 2020-11-19
    Wei-Kai Wu; Suraphan Panyod; Po-Yu Liu; Chieh-Chang Chen; Hsien-Li Kao; Hsiao-Li Chuang; Ying-Hsien Chen; Hsin-Bai Zou; Han-Chun Kuo; Ching-Hua Kuo; Ben-Yang Liao; Tina H. T. Chiu; Ching-Hu Chung; Angela Yu-Chen Lin; Yi-Chia Lee; Sen-Lin Tang; Jin-Town Wang; Yu-Wei Wu; Cheng-Chih Hsu; Lee-Yan Sheen; Alexander N. Orekhov; Ming-Shiang Wu

    The capability of gut microbiota in degrading foods and drugs administered orally can result in diversified efficacies and toxicity interpersonally and cause significant impact on human health. Production of atherogenic trimethylamine N-oxide (TMAO) from carnitine is a gut microbiota-directed pathway and varies widely among individuals. Here, we demonstrated a personalized TMAO formation and carnitine

  • Spatial heterogeneity of bacterial colonization across different gut segments following inter-species microbiota transplantation
    Microbiome (IF 11.607) Pub Date : 2020-11-18
    Na Li; Bin Zuo; Shimeng Huang; Benhua Zeng; Dandan Han; Tiantian Li; Ting Liu; Zhenhua Wu; Hong Wei; Jiangchao Zhao; Junjun Wang

    The microbiota presents a compartmentalized distribution across different gut segments. Hence, the exogenous microbiota from a particular gut segment might only invade its homologous gut location during microbiota transplantation. Feces as the excreted residue contain most of the large-intestinal microbes but lack small-intestinal microbes. We speculated that whole-intestinal microbiota transplantation

  • Association of gut microbiota with metabolism in juvenile Atlantic salmon
    Microbiome (IF 11.607) Pub Date : 2020-11-16
    H. Dvergedal; S. R. Sandve; I. L. Angell; G. Klemetsdal; K. Rudi

    The gut microbiome plays a key role in animal health and metabolism through the intricate functional interconnection between the feed, gut microbes, and the host. Unfortunately, in aquaculture, the links between gut microbes and fish genetics and production phenotypes are not well understood. In this study, we investigate the associations between gut microbial communities, fish feed conversion, and

  • Systemic anti-commensal response to fungi analyzed by flow cytometry is related to gut mycobiome ecology
    Microbiome (IF 11.607) Pub Date : 2020-11-15
    Alicia Moreno-Sabater; Gaelle Autaa; Delphine Sterlin; Amenie Jerbi; Remy Villette; Johanna B. Holm; Christophe Parizot; Sameh Selim; Yaye Senghor; Pascale Ghillani-Dalbin; Claude Bachmeyer; Christophe Hennequin; Guy Gorochov; Martin Larsen

    Interest for the study of gut mycobiota in relation with human health and immune homeostasis has increased in the last years. From this perspective, new tools to study the immune/fungal interface are warranted. Systemic humoral immune responses could reflect the dynamic relationships between gut mycobiota and immunity. Using a novel flow cytometry technology (Fungi-Flow) to determine immunoglobulin

  • Transductomics: sequencing-based detection and analysis of transduced DNA in pure cultures and microbial communities
    Microbiome (IF 11.607) Pub Date : 2020-11-15
    Manuel Kleiner; Brian Bushnell; Kenneth E. Sanderson; Lora V. Hooper; Breck A. Duerkop

    Horizontal gene transfer (HGT) plays a central role in microbial evolution. Our understanding of the mechanisms, frequency, and taxonomic range of HGT in polymicrobial environments is limited, as we currently rely on historical HGT events inferred from genome sequencing and studies involving cultured microorganisms. We lack approaches to observe ongoing HGT in microbial communities. To address this

  • Unravelling the importance of the eukaryotic and bacterial communities and their relationship with Legionella spp. ecology in cooling towers: a complex network
    Microbiome (IF 11.607) Pub Date : 2020-11-12
    Kiran Paranjape; Émilie Bédard; Deeksha Shetty; Mengqi Hu; Fiona Chan Pak Choon; Michèle Prévost; Sébastien P. Faucher

    Cooling towers are a major source of large community-associated outbreaks of Legionnaires’ disease, a severe pneumonia. This disease is contracted when inhaling aerosols that are contaminated with bacteria from the genus Legionella, most importantly Legionella pneumophila. How cooling towers support the growth of this bacterium is still not well understood. As Legionella species are intracellular parasites

  • A comprehensive investigation of metagenome assembly by linked-read sequencing
    Microbiome (IF 11.607) Pub Date : 2020-11-11
    Lu Zhang; Xiaodong Fang; Herui Liao; Zhenmiao Zhang; Xin Zhou; Lijuan Han; Yang Chen; Qinwei Qiu; Shuai Cheng Li

    The human microbiota are complex systems with important roles in our physiological activities and diseases. Sequencing the microbial genomes in the microbiota can help in our interpretation of their activities. The vast majority of the microbes in the microbiota cannot be isolated for individual sequencing. Current metagenomics practices use short-read sequencing to simultaneously sequence a mixture

  • High-quality bacterial genomes of a partial-nitritation/anammox system by an iterative hybrid assembly method
    Microbiome (IF 11.607) Pub Date : 2020-11-06
    Lei Liu; Yulin Wang; You Che; Yiqiang Chen; Yu Xia; Ruibang Luo; Suk Hang Cheng; Chunmiao Zheng; Tong Zhang

    Genome-centric approaches are widely used to investigate microbial compositions, dynamics, ecology, and interactions within various environmental systems. Hundreds or even thousands of genomes could be retrieved in a single study contributed by the cost-effective short-read sequencing and developed assembly/binning pipelines. However, conventional binning methods usually yield highly fragmented draft

  • Shifts in microbial diversity, composition, and functionality in the gut and genital microbiome during a natural SIV infection in vervet monkeys
    Microbiome (IF 11.607) Pub Date : 2020-11-06
    Anna J. Jasinska; Tien S. Dong; Venu Lagishetty; William Katzka; Jonathan P. Jacobs; Christopher A. Schmitt; Jennifer Danzy Cramer; Dongzhu Ma; Willem G. Coetzer; J. Paul Grobler; Trudy R. Turner; Nelson Freimer; Ivona Pandrea; Cristian Apetrei

    The microbiota plays an important role in HIV pathogenesis in humans. Microbiota can impact health through several pathways such as increasing inflammation in the gut, metabolites of bacterial origin, and microbial translocation from the gut to the periphery which contributes to systemic chronic inflammation and immune activation and the development of AIDS. Unlike HIV-infected humans, SIV-infected

  • Alternative stable states in the intestinal ecosystem: proof of concept in a rat model and a perspective of therapeutic implications
    Microbiome (IF 11.607) Pub Date : 2020-11-06
    Maarten Van de Guchte; Sebastian D. Burz; Julie Cadiou; Jiangbo Wu; Stanislas Mondot; Hervé M. Blottière; Joël Doré

    Chronic immune-mediated diseases are rapidly expanding and notoriously difficult to cure. Altered relatively stable intestinal microbiota configurations are associated with several of these diseases, and with a possible pre-disease condition (more susceptible to disease development) of the host-microbiota ecosystem. These observations are reminiscent of the behavior of an ecosystem with alternative

  • Expanding magnetic organelle biogenesis in the domain Bacteria
    Microbiome (IF 11.607) Pub Date : 2020-10-30
    Wei Lin; Wensi Zhang; Greig A. Paterson; Qiyun Zhu; Xiang Zhao; Rob Knight; Dennis A. Bazylinski; Andrew P. Roberts; Yongxin Pan

    The discovery of membrane-enclosed, metabolically functional organelles in Bacteria has transformed our understanding of the subcellular complexity of prokaryotic cells. Biomineralization of magnetic nanoparticles within magnetosomes by magnetotactic bacteria (MTB) is a fascinating example of prokaryotic organelles. Magnetosomes, as nano-sized magnetic sensors in MTB, facilitate cell navigation along

  • Uncovering the genomic potential of the Amazon River microbiome to degrade rainforest organic matter
    Microbiome (IF 11.607) Pub Date : 2020-10-30
    Célio Dias Santos-Júnior; Hugo Sarmento; Fernando Pellon de Miranda; Flávio Henrique-Silva; Ramiro Logares

    The Amazon River is one of the largest in the world and receives huge amounts of terrestrial organic matter (TeOM) from the surrounding rainforest. Despite this TeOM is typically recalcitrant (i.e. resistant to degradation), only a small fraction of it reaches the ocean, pointing to a substantial TeOM degradation by the river microbiome. Yet, microbial genes involved in TeOM degradation in the Amazon

  • Molecular repertoire of Deinococcus radiodurans after 1 year of exposure outside the International Space Station within the Tanpopo mission
    Microbiome (IF 11.607) Pub Date : 2020-10-29
    Emanuel Ott; Yuko Kawaguchi; Denise Kölbl; Elke Rabbow; Petra Rettberg; Maximilian Mora; Christine Moissl-Eichinger; Wolfram Weckwerth; Akihiko Yamagishi; Tetyana Milojevic

    The extraordinarily resistant bacterium Deinococcus radiodurans withstands harsh environmental conditions present in outer space. Deinococcus radiodurans was exposed for 1 year outside the International Space Station within Tanpopo orbital mission to investigate microbial survival and space travel. In addition, a ground-based simulation experiment with conditions, mirroring those from low Earth orbit

  • Parallel and non-parallel changes of the gut microbiota during trophic diversification in repeated young adaptive radiations of sympatric cichlid fish
    Microbiome (IF 11.607) Pub Date : 2020-10-29
    Andreas Härer; Julián Torres-Dowdall; Sina J. Rometsch; Elizabeth Yohannes; Gonzalo Machado-Schiaffino; Axel Meyer

    Recent increases in understanding the ecological and evolutionary roles of microbial communities have underscored the importance of their hosts’ biology. Yet, little is known about gut microbiota dynamics during the early stages of ecological diversification and speciation. We sequenced the V4 region of the 16s rRNA gene to study the gut microbiota of Nicaraguan Midas cichlid fish (Amphilophus cf.

  • Correction to: Hill-based dissimilarity indices and null models for analysis of microbial community assembly
    Microbiome (IF 11.607) Pub Date : 2020-10-28
    Oskar Modin; Raquel Liébana; Soroush Saheb-Alam; Britt-Marie Wilén; Carolina Suarez; Malte Hermansson; Frank Persson

    An amendment to this paper has been published and can be accessed via the original article.

  • Early-life gut dysbiosis linked to juvenile mortality in ostriches
    Microbiome (IF 11.607) Pub Date : 2020-10-12
    Elin Videvall; Se Jin Song; Hanna M. Bensch; Maria Strandh; Anel Engelbrecht; Naomi Serfontein; Olof Hellgren; Adriaan Olivier; Schalk Cloete; Rob Knight; Charlie K. Cornwallis

    Imbalances in the gut microbial community (dysbiosis) of vertebrates have been associated with several gastrointestinal and autoimmune diseases. However, it is unclear which taxa are associated with gut dysbiosis, and if particular gut regions or specific time periods during ontogeny are more susceptible. We also know very little of this process in non-model organisms, despite an increasing realization

  • Ontogeny, species identity, and environment dominate microbiome dynamics in wild populations of kissing bugs (Triatominae)
    Microbiome (IF 11.607) Pub Date : 2020-10-11
    Joel J. Brown; Sonia M. Rodríguez-Ruano; Anbu Poosakkannu; Giampiero Batani; Justin O. Schmidt; Walter Roachell; Jan Zima; Václav Hypša; Eva Nováková

    Kissing bugs (Triatominae) are blood-feeding insects best known as the vectors of Trypanosoma cruzi, the causative agent of Chagas’ disease. Considering the high epidemiological relevance of these vectors, their biology and bacterial symbiosis remains surprisingly understudied. While previous investigations revealed generally low individual complexity but high among-individual variability of the triatomine

  • The interplay between host genetics and the gut microbiome reveals common and distinct microbiome features for complex human diseases
    Microbiome (IF 11.607) Pub Date : 2020-10-08
    Fengzhe Xu; Yuanqing Fu; Ting-yu Sun; Zengliang Jiang; Zelei Miao; Menglei Shuai; Wanglong Gou; Chu-wen Ling; Jian Yang; Jun Wang; Yu-ming Chen; Ju-Sheng Zheng

    Interest in the interplay between host genetics and the gut microbiome in complex human diseases is increasing, with prior evidence mainly being derived from animal models. In addition, the shared and distinct microbiome features among complex human diseases remain largely unclear. This analysis was based on a Chinese population with 1475 participants. We estimated the SNP-based heritability, which

  • Viral ecogenomics across the Porifera
    Microbiome (IF 11.607) Pub Date : 2020-10-02
    Cecília Pascelli; Patrick W. Laffy; Emmanuelle Botté; Marija Kupresanin; Thomas Rattei; Miguel Lurgi; Timothy Ravasi; Nicole S. Webster

    Viruses directly affect the most important biological processes in the ocean via their regulation of prokaryotic and eukaryotic populations. Marine sponges form stable symbiotic partnerships with a wide diversity of microorganisms and this high symbiont complexity makes them an ideal model for studying viral ecology. Here, we used morphological and molecular approaches to illuminate the diversity and

  • β-glucan attenuates cognitive impairment via the gut-brain axis in diet-induced obese mice
    Microbiome (IF 11.607) Pub Date : 2020-10-02
    Hongli Shi; Yinghua Yu; Danhong Lin; Peng Zheng; Peng Zhang; Minmin Hu; Qiao Wang; Wei Pan; Xiaoying Yang; Tao Hu; Qianqian Li; Renxian Tang; Feng Zhou; Kuiyang Zheng; Xu-Feng Huang

    “Western” style dietary patterns are characterized by a high proportion of highly processed foods rich in fat and low in fiber. This diet pattern is associated with a myriad of metabolic dysfunctions, including neuroinflammation and cognitive impairment. β-glucan, the major soluble fiber in oat and barley grains, is fermented in the lower gastrointestinal tract, potentially impacting the microbial

  • Trophic interactions as determinants of the arbuscular mycorrhizal fungal community with cascading plant-promoting consequences
    Microbiome (IF 11.607) Pub Date : 2020-10-02
    Yuji Jiang; Lu Luan; Kaijie Hu; Manqiang Liu; Ziyun Chen; Stefan Geisen; Xiaoyun Chen; Huixin Li; Qinsong Xu; Michael Bonkowski; Bo Sun

    The soil mycobiome is composed of a complex and diverse fungal community, which includes functionally diverse species ranging from plant pathogens to mutualists. Among the latter are arbuscular mycorrhizal fungi (AMF) that provide phosphorous (P) to plants. While plant hosts and abiotic parameters are known to structure AMF communities, it remains largely unknown how higher trophic level organisms

  • Investigating host-microbiome interactions by droplet based microfluidics
    Microbiome (IF 11.607) Pub Date : 2020-10-01
    Alexandra S. Tauzin; Mariana Rangel Pereira; Liisa D. Van Vliet; Pierre-Yves Colin; Elisabeth Laville; Jeremy Esque; Sandrine Laguerre; Bernard Henrissat; Nicolas Terrapon; Vincent Lombard; Marion Leclerc; Joël Doré; Florian Hollfelder; Gabrielle Potocki-Veronese

    Despite the importance of the mucosal interface between microbiota and the host in gut homeostasis, little is known about the mechanisms of bacterial gut colonization, involving foraging for glycans produced by epithelial cells. The slow pace of progress toward understanding the underlying molecular mechanisms is largely due to the lack of efficient discovery tools, especially those targeting the uncultured

  • Faecal microbiota transplant from aged donor mice affects spatial learning and memory via modulating hippocampal synaptic plasticity- and neurotransmission-related proteins in young recipients
    Microbiome (IF 11.607) Pub Date : 2020-10-01
    Alfonsina D’Amato; Lorenzo Di Cesare Mannelli; Elena Lucarini; Angela L. Man; Gwenaelle Le Gall; Jacopo J. V. Branca; Carla Ghelardini; Amedeo Amedei; Eugenio Bertelli; Mari Regoli; Alessandra Pacini; Giulia Luciani; Pasquale Gallina; Annalisa Altera; Arjan Narbad; Massimo Gulisano; Lesley Hoyles; David Vauzour; Claudio Nicoletti

    The gut-brain axis and the intestinal microbiota are emerging as key players in health and disease. Shifts in intestinal microbiota composition affect a variety of systems; however, evidence of their direct impact on cognitive functions is still lacking. We tested whether faecal microbiota transplant (FMT) from aged donor mice into young adult recipients altered the hippocampus, an area of the central

  • Soil origin and plant genotype structure distinct microbiome compartments in the model legume Medicago truncatula
    Microbiome (IF 11.607) Pub Date : 2020-09-28
    Shawn P. Brown; Michael A. Grillo; Justin C. Podowski; Katy D. Heath

    Understanding the genetic and environmental factors that structure plant microbiomes is necessary for leveraging these interactions to address critical needs in agriculture, conservation, and sustainability. Legumes, which form root nodule symbioses with nitrogen-fixing rhizobia, have served as model plants for understanding the genetics and evolution of beneficial plant-microbe interactions for decades

  • Disruption of ruminal homeostasis by malnutrition involved in systemic ruminal microbiota-host interactions in a pregnant sheep model
    Microbiome (IF 11.607) Pub Date : 2020-09-24
    Yanfeng Xue; Limei Lin; Fan Hu; Weiyun Zhu; Shengyong Mao

    Undernutrition is a prevalent and spontaneous condition in animal production which always affects microbiota-host interaction in gastrointestinal tract. However, how undernutrition affects crosstalk homeostasis is largely unknown. Here, we discover how undernutrition affects microbial profiles and subsequently how microbial metabolism affects the signal transduction and tissue renewal in ruminal epithelium

  • Bio-organic fertilizers stimulate indigenous soil Pseudomonas populations to enhance plant disease suppression.
    Microbiome (IF 11.607) Pub Date : 2020-09-22
    Chengyuan Tao,Rong Li,Wu Xiong,Zongzhuan Shen,Shanshan Liu,Beibei Wang,Yunze Ruan,Stefan Geisen,Qirong Shen,George A Kowalchuk

    Plant diseases caused by fungal pathogen result in a substantial economic impact on the global food and fruit industry. Application of organic fertilizers supplemented with biocontrol microorganisms (i.e. bioorganic fertilizers) has been shown to improve resistance against plant pathogens at least in part due to impacts on the structure and function of the resident soil microbiome. However, it remains

  • Gut microbiota steroid sexual dimorphism and its impact on gonadal steroids: influences of obesity and menopausal status.
    Microbiome (IF 11.607) Pub Date : 2020-09-20
    Jordi Mayneris-Perxachs,María Arnoriaga-Rodríguez,Diego Luque-Córdoba,Feliciano Priego-Capote,Vicente Pérez-Brocal,Andrés Moya,Aurelijus Burokas,Rafael Maldonado,José-Manuel Fernández-Real

    Gonadal steroid hormones have been suggested as the underlying mechanism responsible for the sexual dimorphism observed in metabolic diseases. Animal studies have also evidenced a causal role of the gut microbiome and metabolic health. However, the role of sexual dimorphism in the gut microbiota and the potential role of the microbiome in influencing sex steroid hormones and shaping sexually dimorphic

  • Microbial dark matter filling the niche in hypersaline microbial mats.
    Microbiome (IF 11.607) Pub Date : 2020-09-16
    Hon Lun Wong,Fraser I MacLeod,Richard Allen White,Pieter T Visscher,Brendan P Burns

    Shark Bay, Australia, harbours one of the most extensive and diverse systems of living microbial mats that are proposed to be analogs of some of the earliest ecosystems on Earth. These ecosystems have been shown to possess a substantial abundance of uncultivable microorganisms. These enigmatic microbes, jointly coined as ‘microbial dark matter’ (MDM), are hypothesised to play key roles in modern microbial

  • Estimate of the sequenced proportion of the global prokaryotic genome.
    Microbiome (IF 11.607) Pub Date : 2020-09-16
    Zheng Zhang,Jianing Wang,Jinlan Wang,Jingjing Wang,Yuezhong Li

    Sequencing prokaryotic genomes has revolutionized our understanding of the many roles played by microorganisms. However, the cell and taxon proportions of genome-sequenced bacteria or archaea on earth remain unknown. This study aimed to explore this basic question using large-scale alignment between the sequences released by the Earth Microbiome Project and 155,810 prokaryotic genomes from public databases

  • Antibiotics create a shift from mutualism to competition in human gut communities with a longer-lasting impact on fungi than bacteria.
    Microbiome (IF 11.607) Pub Date : 2020-09-12
    Bastian Seelbinder,Jiarui Chen,Sascha Brunke,Ruben Vazquez-Uribe,Rakesh Santhaman,Anne-Christin Meyer,Felipe Senne de Oliveira Lino,Ka-Fai Chan,Daniel Loos,Lejla Imamovic,Chi-Ching Tsang,Rex Pui-Kin Lam,Siddharth Sridhar,Kang Kang,Bernhard Hube,Patrick Chiu-Yat Woo,Morten Otto Alexander Sommer,Gianni Panagiotou

    Antibiotic treatment has a well-established detrimental effect on the gut bacterial composition, but effects on the fungal community are less clear. Bacteria in the lumen of the gastrointestinal tract may limit fungal colonization and invasion. Antibiotic drugs targeting bacteria are therefore seen as an important risk factor for fungal infections and induced allergies. However, antibiotic effects

  • Hill-based dissimilarity indices and null models for analysis of microbial community assembly.
    Microbiome (IF 11.607) Pub Date : 2020-09-11
    Oskar Modin,Raquel Liébana,Soroush Saheb-Alam,Britt-Marie Wilén,Carolina Suarez,Malte Hermansson,Frank Persson

    High-throughput amplicon sequencing of marker genes, such as the 16S rRNA gene in Bacteria and Archaea, provides a wealth of information about the composition of microbial communities. To quantify differences between samples and draw conclusions about factors affecting community assembly, dissimilarity indices are typically used. However, results are subject to several biases, and data interpretation

  • Identification of multidimensional Boolean patterns in microbial communities.
    Microbiome (IF 11.607) Pub Date : 2020-09-11
    George Golovko,Khanipov Kamil,Levent Albayrak,Anna M Nia,Renato Salomon Arroyo Duarte,Sergei Chumakov,Yuriy Fofanov

    Identification of complex multidimensional interaction patterns within microbial communities is the key to understand, modulate, and design beneficial microbiomes. Every community has members that fulfill an essential function affecting multiple other community members through secondary metabolism. Since microbial community members are often simultaneously involved in multiple relations, not all interaction

  • Multi-omics analysis reveals the influence of genetic and environmental risk factors on developing gut microbiota in infants at risk of celiac disease.
    Microbiome (IF 11.607) Pub Date : 2020-09-11
    Maureen M Leonard,Hiren Karathia,Meritxell Pujolassos,Jacopo Troisi,Francesco Valitutti,Poorani Subramanian,Stephanie Camhi,Victoria Kenyon,Angelo Colucci,Gloria Serena,Salvatore Cucchiara,Monica Montuori,Basilio Malamisura,Ruggiero Francavilla,Luca Elli,Brian Fanelli,Rita Colwell,Nur Hasan,Ali R Zomorrodi,Alessio Fasano,

    Celiac disease (CD) is an autoimmune digestive disorder that occurs in genetically susceptible individuals in response to ingesting gluten, a protein found in wheat, rye, and barley. Research shows that genetic predisposition and exposure to gluten are necessary but not sufficient to trigger the development of CD. This suggests that exposure to other environmental stimuli early in life, e.g., cesarean

  • Maternal gut microbes shape the early-life assembly of gut microbiota in passerine chicks via nests.
    Microbiome (IF 11.607) Pub Date : 2020-09-11
    Cheng-Yu Chen,Chih-Kuan Chen,Yi-Ying Chen,Andrew Fang,Grace Tzun-Wen Shaw,Chih-Ming Hung,Daryi Wang

    Knowledge is growing on how gut microbiota are established, but the effects of maternal symbiotic microbes throughout early microbial successions in birds remain elusive. In this study, we examined the contributions and transmission modes of maternal microbes into the neonatal microbiota of a passerine, the zebra finch (Taeniopygia guttata), based on fostering experiments. Using 16S rRNA amplicon sequencing

  • Impact of industrial production system parameters on chicken microbiomes: mechanisms to improve performance and reduce Campylobacter.
    Microbiome (IF 11.607) Pub Date : 2020-09-09
    Aaron McKenna,Umer Zeeshan Ijaz,Carmel Kelly,Mark Linton,William T Sloan,Brian D Green,Ursula Lavery,Nick Dorrell,Brendan W Wren,Anne Richmond,Nicolae Corcionivoschi,Ozan Gundogdu

    The factors affecting host-pathogen ecology in terms of the microbiome remain poorly studied. Chickens are a key source of protein with gut health heavily dependent on the complex microbiome which has key roles in nutrient assimilation and vitamin and amino acid biosynthesis. The chicken gut microbiome may be influenced by extrinsic production system parameters such as Placement Birds/m2 (stocking

  • Nanoparticle treatment of maize analyzed through the metatranscriptome: compromised nitrogen cycling, possible phytopathogen selection, and plant hormesis.
    Microbiome (IF 11.607) Pub Date : 2020-09-09
    Wouter M A Sillen,Sofie Thijs,Gennaro Roberto Abbamondi,Roberto De La Torre Roche,Nele Weyens,Jason C White,Jaco Vangronsveld

    The beneficial use of nanoparticle silver or nanosilver may be confounded when its potent antimicrobial properties impact non-target members of natural microbiomes such as those present in soil or the plant rhizosphere. Agricultural soils are a likely sink for nanosilver due to its presence in agrochemicals and land-applied biosolids, but a complete assessment of nanosilver’s effects on this environment

  • Bradymonabacteria, a novel bacterial predator group with versatile survival strategies in saline environments.
    Microbiome (IF 11.607) Pub Date : 2020-08-31
    Da-Shuai Mu,Shuo Wang,Qi-Yun Liang,Zhao-Zhong Du,Renmao Tian,Yang Ouyang,Xin-Peng Wang,Aifen Zhou,Ya Gong,Guan-Jun Chen,Joy Van Nostrand,Yunfeng Yang,Jizhong Zhou,Zong-Jun Du

    Bacterial predation is an important selective force in microbial community structure and dynamics. However, only a limited number of predatory bacteria have been reported, and their predatory strategies and evolutionary adaptations remain elusive. We recently isolated a novel group of bacterial predators, Bradymonabacteria, representative of the novel order Bradymonadales in δ-Proteobacteria. Compared

  • Impact of investigational microbiota therapeutic RBX2660 on the gut microbiome and resistome revealed by a placebo-controlled clinical trial.
    Microbiome (IF 11.607) Pub Date : 2020-08-31
    Suryang Kwak,JooHee Choi,Tiffany Hink,Kimberly A Reske,Kenneth Blount,Courtney Jones,Margaret H Bost,Xiaoqing Sun,Carey-Ann D Burnham,Erik R Dubberke,Gautam Dantas,

    Intestinal microbiota restoration can be achieved by complementing a subject’s perturbed microbiota with that of a healthy donor. Recurrent Clostridioides difficile infection (rCDI) is one key application of such treatment. Another emerging application of interest is reducing antibiotic-resistant genes (ARGs) and organisms (AROs). In this study, we investigated fecal specimens from a multicenter, randomized

  • Ultrafast and accurate 16S rRNA microbial community analysis using Kraken 2.
    Microbiome (IF 11.607) Pub Date : 2020-08-28
    Jennifer Lu,Steven L Salzberg

    For decades, 16S ribosomal RNA sequencing has been the primary means for identifying the bacterial species present in a sample with unknown composition. One of the most widely used tools for this purpose today is the QIIME (Quantitative Insights Into Microbial Ecology) package. Recent results have shown that the newest release, QIIME 2, has higher accuracy than QIIME, MAPseq, and mothur when classifying

  • A ubiquitous subcuticular bacterial symbiont of a coral predator, the crown-of-thorns starfish, in the Indo-Pacific.
    Microbiome (IF 11.607) Pub Date : 2020-08-24
    Naohisa Wada,Hideaki Yuasa,Rei Kajitani,Yasuhiro Gotoh,Yoshitoshi Ogura,Dai Yoshimura,Atsushi Toyoda,Sen-Lin Tang,Yukihiro Higashimura,Hugh Sweatman,Zac Forsman,Omri Bronstein,Gal Eyal,Nalinee Thongtham,Takehiko Itoh,Tetsuya Hayashi,Nina Yasuda

    Population outbreaks of the crown-of-thorns starfish (Acanthaster planci sensu lato; COTS), a primary predator of reef-building corals in the Indo-Pacific Ocean, are a major threat to coral reefs. While biological and ecological knowledge of COTS has been accumulating since the 1960s, little is known about its associated bacteria. The aim of this study was to provide fundamental information on the

  • Protoblock - A biological standard for formalin fixed samples.
    Microbiome (IF 11.607) Pub Date : 2020-08-22
    Yensi Flores Bueso,Sidney P Walker,Glenn Hogan,Marcus J Claesson,Mark Tangney

    Formalin-fixed, paraffin-embedded (FFPE) tissue is the gold standard in pathology tissue storage, representing the largest collections of patient material. Their reliable use for DNA analyses could open a trove of potential samples for research and are currently being recognised as a viable source material for bacterial analysis. There are several key features which limit bacterial-related data generation

  • Antimicrobial drug use in the first decade of life influences saliva microbiota diversity and composition.
    Microbiome (IF 11.607) Pub Date : 2020-08-21
    Sajan C Raju,Heli Viljakainen,Rejane A O Figueiredo,Pertti J Neuvonen,Johan G Eriksson,Elisabete Weiderpass,Trine B Rounge

    The human microbiota contributes to health and well-being. Antimicrobials (AM) have an immediate effect on microbial diversity and composition in the gut, but next to nothing is known about their long-term contribution to saliva microbiota. Our objectives were to investigate the long-term impact of AM use on saliva microbiota diversity and composition in preadolescents. We compared the lifetime effects

  • The gut microbiota regulates autism-like behavior by mediating vitamin B6 homeostasis in EphB6-deficient mice.
    Microbiome (IF 11.607) Pub Date : 2020-08-20
    Ying Li,Zheng-Yi Luo,Yu-Ying Hu,Yue-Wei Bi,Jian-Ming Yang,Wen-Jun Zou,Yun-Long Song,Shi Li,Tong Shen,Shu-Ji Li,Lang Huang,Ai-Jun Zhou,Tian-Ming Gao,Jian-Ming Li

    Autism spectrum disorder (ASD) is a developmental disorder, and the effective pharmacological treatments for the core autistic symptoms are currently limited. Increasing evidence, particularly that from clinical studies on ASD patients, suggests a functional link between the gut microbiota and the development of ASD. However, the mechanisms linking the gut microbiota with brain dysfunctions (gut-brain

  • Correction to: Microbiome definition re-visited: old concepts and new challenges.
    Microbiome (IF 11.607) Pub Date : 2020-08-20
    Gabriele Berg,Daria Rybakova,Doreen Fischer,Tomislav Cernava,Marie-Christine Champomier Vergès,Trevor Charles,Xiaoyulong Chen,Luca Cocolin,Kellye Eversole,Gema Herrero Corral,Maria Kazou,Linda Kinkel,Lene Lange,Nelson Lima,Alexander Loy,James A Macklin,Emmanuelle Maguin,Tim Mauchline,Ryan McClure,Birgit Mitter,Matthew Ryan,Inga Sarand,Hauke Smidt,Bettina Schelkle,Hugo Roume,G Seghal Kiran,Joseph Selvin

    An amendment to this paper has been published and can be accessed via the original article.

  • Gut microbiota modulation with long-chain corn bran arabinoxylan in adults with overweight and obesity is linked to an individualized temporal increase in fecal propionate.
    Microbiome (IF 11.607) Pub Date : 2020-08-19
    Nguyen K Nguyen,Edward C Deehan,Zhengxiao Zhang,Mingliang Jin,Nami Baskota,Maria Elisa Perez-Muñoz,Janis Cole,Yunus E Tuncil,Benjamin Seethaler,Ting Wang,Martine Laville,Nathalie M Delzenne,Stephan C Bischoff,Bruce R Hamaker,Inés Martínez,Dan Knights,Jeffrey A Bakal,Carla M Prado,Jens Walter

    Variability in the health effects of dietary fiber might arise from inter-individual differences in the gut microbiota’s ability to ferment these substrates into beneficial metabolites. Our understanding of what drives this individuality is vastly incomplete and will require an ecological perspective as microbiomes function as complex inter-connected communities. Here, we performed a parallel two-arm

  • "Microbiota, symbiosis and individuality summer school" meeting report.
    Microbiome (IF 11.607) Pub Date : 2020-08-14
    Isobel Ronai,Gregor P Greslehner,Federico Boem,Judith Carlisle,Adrian Stencel,Javier Suárez,Saliha Bayir,Wiebke Bretting,Joana Formosinho,Anna C Guerrero,William H Morgan,Cybèle Prigot-Maurice,Salome Rodeck,Marie Vasse,Jacqueline M Wallis,Oryan Zacks

    How does microbiota research impact our understanding of biological individuality? We summarize the interdisciplinary summer school on “Microbiota, symbiosis and individuality: conceptual and philosophical issues” (July 2019), which was supported by a European Research Council starting grant project “Immunity, DEvelopment, and the Microbiota” (IDEM). The summer school centered around interdisciplinary

  • Influence of the polar light cycle on seasonal dynamics of an Antarctic lake microbial community.
    Microbiome (IF 11.607) Pub Date : 2020-08-09
    Pratibha Panwar,Michelle A Allen,Timothy J Williams,Alyce M Hancock,Sarah Brazendale,James Bevington,Simon Roux,David Páez-Espino,Stephen Nayfach,Maureen Berg,Frederik Schulz,I-Min A Chen,Marcel Huntemann,Nicole Shapiro,Nikos C Kyrpides,Tanja Woyke,Emiley A Eloe-Fadrosh,Ricardo Cavicchioli

    Cold environments dominate the Earth’s biosphere and microbial activity drives ecosystem processes thereby contributing greatly to global biogeochemical cycles. Polar environments differ to all other cold environments by experiencing 24-h sunlight in summer and no sunlight in winter. The Vestfold Hills in East Antarctica contains hundreds of lakes that have evolved from a marine origin only 3000–7000 years

  • Environmental shaping of the bacterial and fungal community in infant bed dust and correlations with the airway microbiota.
    Microbiome (IF 11.607) Pub Date : 2020-08-07
    Shashank Gupta,Mathis H Hjelmsø,Jenni Lehtimäki,Xuanji Li,Martin S Mortensen,Jakob Russel,Urvish Trivedi,Morten A Rasmussen,Jakob Stokholm,Hans Bisgaard,Søren J Sørensen

    From early life, children are exposed to a multitude of environmental exposures, which may be of crucial importance for healthy development. Here, the environmental microbiota may be of particular interest as it represents the interface between environmental factors and the child. As infants in modern societies spend a considerable amount of time indoors, we hypothesize that the indoor bed dust microbiota

  • The human gut archaeome: identification of diverse haloarchaea in Korean subjects.
    Microbiome (IF 11.607) Pub Date : 2020-08-04
    Joon Yong Kim,Tae Woong Whon,Mi Young Lim,Yeon Bee Kim,Namhee Kim,Min-Sung Kwon,Juseok Kim,Se Hee Lee,Hak-Jong Choi,In-Hyun Nam,Won-Hyong Chung,Jung-Ha Kim,Jin-Woo Bae,Seong Woon Roh,Young-Do Nam

    Archaea are one of the least-studied members of the gut-dwelling autochthonous microbiota. Few studies have reported the dominance of methanogens in the archaeal microbiome (archaeome) of the human gut, although limited information regarding the diversity and abundance of other archaeal phylotypes is available. We surveyed the archaeome of faecal samples collected from 897 East Asian subjects living

  • Immunoglobulin recognition of fecal bacteria in stunted and non-stunted children: findings from the Afribiota study.
    Microbiome (IF 11.607) Pub Date : 2020-07-27
    Kelsey E Huus,André Rodriguez-Pozo,Nathalie Kapel,Alison Nestoret,Azimdine Habib,Michel Dede,Amee Manges,Jean-Marc Collard,Philippe J Sansonetti,Pascale Vonaesch,B Brett Finlay,

    Child undernutrition is a global health issue that is associated with poor sanitation and an altered intestinal microbiota. Immunoglobulin (Ig) A mediates host-microbial homeostasis in the intestine, and acutely undernourished children have been shown to have altered IgA recognition of the fecal microbiota. We sought to determine whether chronic undernutrition (stunting) or intestinal inflammation

  • Microbiota from alginate oligosaccharide-dosed mice successfully mitigated small intestinal mucositis.
    Microbiome (IF 11.607) Pub Date : 2020-07-25
    Pengfei Zhang,Jing Liu,Bohui Xiong,Cong Zhang,Beining Kang,Yishan Gao,Zengkuan Li,Wei Ge,Shunfeng Cheng,Yanan Hao,Wei Shen,Shuai Yu,Liang Chen,Xiangfang Tang,Yong Zhao,Hongfu Zhang

    The increasing incidence of cancer and intestinal mucositis induced by chemotherapeutics are causing worldwide concern. Many approaches such as fecal microbiota transplantation (FMT) have been used to minimize mucositis. However, it is still unknown whether FMT from a donor with beneficial gut microbiota results in more effective intestinal function in the recipient. Recently, we found that alginate