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  • 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

  • Catabolism and interactions of uncultured organisms shaped by eco-thermodynamics in methanogenic bioprocesses.
    Microbiome (IF 11.607) Pub Date : 2020-07-24
    Masaru K Nobu,Takashi Narihiro,Ran Mei,Yoichi Kamagata,Patrick K H Lee,Po-Heng Lee,Michael J McInerney,Wen-Tso Liu

    Current understanding of the carbon cycle in methanogenic environments involves trophic interactions such as interspecies H2 transfer between organotrophs and methanogens. However, many metabolic processes are thermodynamically sensitive to H2 accumulation and can be inhibited by H2 produced from co-occurring metabolisms. Strategies for driving thermodynamically competing metabolisms in methanogenic

  • Gut microbiome composition differences among breeds impact feed efficiency in swine.
    Microbiome (IF 11.607) Pub Date : 2020-07-22
    Matteo Bergamaschi,Francesco Tiezzi,Jeremy Howard,Yi Jian Huang,Kent A Gray,Constantino Schillebeeckx,Nathan P McNulty,Christian Maltecca

    Feed efficiency is a crucial parameter in swine production, given both its economic and environmental impact. The gut microbiota plays an essential role in nutrient digestibility and is, therefore, likely to affect feed efficiency. This study aimed to characterize feed efficiency, fatness traits, and gut microbiome composition in three major breeds of domesticated swine and investigate a possible link

  • Correction to: Temporal transcriptional patterns of cyanophage genes suggest synchronized infection of cyanobacteria in the oceans.
    Microbiome (IF 11.607) Pub Date : 2020-07-16
    Yue Chen,Qinglu Zeng

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

  • Bacteria pathogens drive host colonic epithelial cell promoter hypermethylation of tumor suppressor genes in colorectal cancer.
    Microbiome (IF 11.607) Pub Date : 2020-07-16
    Xiaoxuan Xia,William Ka Kei Wu,Sunny Hei Wong,Dabin Liu,Thomas Ngai Yeung Kwong,Geicho Nakatsu,Pearlly S Yan,Yu-Ming Chuang,Michael Wing-Yan Chan,Olabisi Oluwabukola Coker,Zigui Chen,Yun Kit Yeoh,Liuyang Zhao,Xiansong Wang,Wing Yin Cheng,Matthew Tak Vai Chan,Paul Kay Sheung Chan,Joseph Jao Yiu Sung,Maggie Haitian Wang,Jun Yu

    Altered microbiome composition and aberrant promoter hypermethylation of tumor suppressor genes (TSGs) are two important hallmarks of colorectal cancer (CRC). Here we performed concurrent 16S rRNA gene sequencing and methyl-CpG binding domain-based capture sequencing in 33 tissue biopsies (5 normal colonic mucosa tissues, 4 pairs of adenoma and adenoma-adjacent tissues, and 10 pairs of CRC and CRC-adjacent

  • The extracellular vesicle of gut microbial Paenalcaligenes hominis is a risk factor for vagus nerve-mediated cognitive impairment.
    Microbiome (IF 11.607) Pub Date : 2020-07-15
    Kyung-Eon Lee,Jeon-Kyung Kim,Sang-Kap Han,Dong Yun Lee,Hae-Ji Lee,Sung-Vin Yim,Dong-Hyun Kim

    In a pilot study, we found that feces transplantation from elderly individuals to mice significantly caused cognitive impairment. Paenalcaligenes hominis and Escherichia coli are increasingly detected in the feces of elderly adults and aged mice. Therefore, we isolated Paenalcaligenes hominis and Escherichia coli from the feces of elderly individuals and aged mice and examined their effects on the

  • Fine-scale succession patterns and assembly mechanisms of bacterial community of Litopenaeus vannamei larvae across the developmental cycle.
    Microbiome (IF 11.607) Pub Date : 2020-07-03
    Yanting Wang,Kai Wang,Lei Huang,Pengsheng Dong,Sipeng Wang,Heping Chen,Zheng Lu,Dandi Hou,Demin Zhang

    Microbiome assembly in early life may have a long-term impact on host health. Larval nursery is a crucial period that determines the success in culture of Litopenaeus vannamei, the most productive shrimp species in world aquaculture industry. However, the succession patterns and assembly mechanisms of larval shrimp bacterial community still lack characterization at a fine temporal scale. Here, using

  • Syntrophic acetate oxidation replaces acetoclastic methanogenesis during thermophilic digestion of biowaste.
    Microbiome (IF 11.607) Pub Date : 2020-07-03
    Stefan Dyksma,Lukas Jansen,Claudia Gallert

    Anaerobic digestion (AD) is a globally important technology for effective waste and wastewater management. In AD, microorganisms interact in a complex food web for the production of biogas. Here, acetoclastic methanogens and syntrophic acetate-oxidizing bacteria (SAOB) compete for acetate, a major intermediate in the mineralization of organic matter. Although evidence is emerging that syntrophic acetate

  • Recent infection by Wolbachia alters microbial communities in wild Laodelphax striatellus populations.
    Microbiome (IF 11.607) Pub Date : 2020-07-02
    Xing-Zhi Duan,Jing-Tao Sun,Lin-Ting Wang,Xiao-Han Shu,Yan Guo,Matsukura Keiichiro,Yu-Xi Zhu,Xiao-Li Bing,Ary A Hoffmann,Xiao-Yue Hong

    Host-associated microbial communities play an important role in the fitness of insect hosts. However, the factors shaping microbial communities in wild populations, including genetic background, ecological factors, and interactions among microbial species, remain largely unknown. Here, we surveyed microbial communities of the small brown planthopper (SBPH, Laodelphax striatellus) across 17 geographical

  • Microbiome definition re-visited: old concepts and new challenges.
    Microbiome (IF 11.607) Pub Date : 2020-06-30
    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

    The field of microbiome research has evolved rapidly over the past few decades and has become a topic of great scientific and public interest. As a result of this rapid growth in interest covering different fields, we are lacking a clear commonly agreed definition of the term “microbiome.” Moreover, a consensus on best practices in microbiome research is missing. Recently, a panel of international

  • Microbial succession during the transition from active to inactive stages of deep-sea hydrothermal vent sulfide chimneys.
    Microbiome (IF 11.607) Pub Date : 2020-06-30
    Jialin Hou,Stefan M Sievert,Yinzhao Wang,Jeffrey S Seewald,Vengadesh Perumal Natarajan,Fengping Wang,Xiang Xiao

    Deep-sea hydrothermal vents are highly productive biodiversity hotspots in the deep ocean supported by chemosynthetic microorganisms. Prominent features of these systems are sulfide chimneys emanating high-temperature hydrothermal fluids. While several studies have investigated the microbial diversity in both active and inactive sulfide chimneys that have been extinct for up to thousands of years,

  • Correction to: The microbiome as a biosensor: functional profiles elucidate hidden stress in hosts.
    Microbiome (IF 11.607) Pub Date : 2020-06-30
    Avihai Zolti,Stefan J Green,Noa Sela,Yitzhak Hadar,Dror Minz

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

  • Changes of the human skin microbiota upon chronic exposure to polycyclic aromatic hydrocarbon pollutants.
    Microbiome (IF 11.607) Pub Date : 2020-06-26
    Marcus H Y Leung,Xinzhao Tong,Philippe Bastien,Florent Guinot,Arthur Tenenhaus,Brice M R Appenzeller,Richard J Betts,Sakina Mezzache,Jing Li,Nasrine Bourokba,Lionel Breton,Cécile Clavaud,Patrick K H Lee

    Polycyclic aromatic hydrocarbons (PAHs) are of environmental and public health concerns and contribute to adverse skin attributes such as premature skin aging and pigmentary disorder. However, little information is available on the potential roles of chronic urban PAH pollutant exposure on the cutaneous microbiota. Given the roles of the skin microbiota have on healthy and undesirable skin phenotypes

  • Reservoirs of antimicrobial resistance genes in retail raw milk.
    Microbiome (IF 11.607) Pub Date : 2020-06-26
    Jinxin Liu,Yuanting Zhu,Michele Jay-Russell,Danielle G Lemay,David A Mills

    It has been estimated that at least 3% of the USA population consumes unpasteurized (raw) milk from animal sources, and the demand to legalize raw milk sales continues to increase. However, consumption of raw milk can cause foodborne illness and be a source of bacteria containing transferrable antimicrobial resistance genes (ARGs). To obtain a comprehensive understanding of the microbiome and antibiotic

  • Developing standards for the microbiome field.
    Microbiome (IF 11.607) Pub Date : 2020-06-26
    Gregory C A Amos,Alastair Logan,Saba Anwar,Martin Fritzsche,Ryan Mate,Thomas Bleazard,Sjoerd Rijpkema

    Effective standardisation of methodologies to analyse the microbiome is essential to the entire microbiome community. Despite the microbiome field being established for over a decade, there are no accredited or certified reference materials available to the wider community. In this study, we describe the development of the first reference reagents produced by the National Institute for Biological Standards

  • Revealing the microbial assemblage structure in the human gut microbiome using latent Dirichlet allocation.
    Microbiome (IF 11.607) Pub Date : 2020-06-23
    Shion Hosoda,Suguru Nishijima,Tsukasa Fukunaga,Masahira Hattori,Michiaki Hamada

    The human gut microbiome has been suggested to affect human health and thus has received considerable attention. To clarify the structure of the human gut microbiome, clustering methods are frequently applied to human gut taxonomic profiles. Enterotypes, i.e., clusters of individuals with similar microbiome composition, are well-studied and characterized. However, only a few detailed studies on assemblages

  • A genomic view of trophic and metabolic diversity in clade-specific Lamellodysidea sponge microbiomes.
    Microbiome (IF 11.607) Pub Date : 2020-06-23
    Sheila Podell,Jessica M Blanton,Aaron Oliver,Michelle A Schorn,Vinayak Agarwal,Jason S Biggs,Bradley S Moore,Eric E Allen

    Marine sponges and their microbiomes contribute significantly to carbon and nutrient cycling in global reefs, processing and remineralizing dissolved and particulate organic matter. Lamellodysidea herbacea sponges obtain additional energy from abundant photosynthetic Hormoscilla cyanobacterial symbionts, which also produce polybrominated diphenyl ethers (PBDEs) chemically similar to anthropogenic pollutants

  • Compositional and functional characterisation of biomass-degrading microbial communities in guts of plant fibre- and soil-feeding higher termites.
    Microbiome (IF 11.607) Pub Date : 2020-06-23
    Martyna Marynowska,Xavier Goux,David Sillam-Dussès,Corinne Rouland-Lefèvre,Rashi Halder,Paul Wilmes,Piotr Gawron,Yves Roisin,Philippe Delfosse,Magdalena Calusinska

    Termites are among the most successful insect lineages on the globe and are responsible for providing numerous ecosystem services. They mainly feed on wood and other plant material at different stages of humification. Lignocellulose is often a principal component of such plant diet, and termites largely rely on their symbiotic microbiota and associated enzymes to decompose their food efficiently. While

  • Genomic and transcriptomic insights into methanogenesis potential of novel methanogens from mangrove sediments.
    Microbiome (IF 11.607) Pub Date : 2020-06-17
    Cui-Jing Zhang,Jie Pan,Yang Liu,Chang-Hai Duan,Meng Li

    Methanogens are crucial to global methane budget and carbon cycling. Methanogens from the phylum Euryarchaeota are currently classified into one class and seven orders, including two novel methanogen taxa, Methanofastidiosa and Methanomassiliicoccales. The relative importance of the novel methanogens to methane production in the natural environment is poorly understood. Here, we used a combined metagenomic

  • The skin microbiome of elasmobranchs follows phylosymbiosis, but in teleost fishes, the microbiomes converge.
    Microbiome (IF 11.607) Pub Date : 2020-06-13
    Michael P Doane,Megan M Morris,Bhavya Papudeshi,Lauren Allen,Dnyanada Pande,John M Haggerty,Shaili Johri,Abigail C Turnlund,Meredith Peterson,Dovi Kacev,Andy Nosal,Deni Ramirez,Kevin Hovel,Julia Ledbetter,Amanda Alker,Jackeline Avalos,Kristi Baker,Shruti Bhide,Emma Billings,Steven Byrum,Molly Clemens,Amelia Juliette Demery,Lais Farias Oliveira Lima,Oscar Gomez,Omar Gutierrez,Selena Hinton,Donald Kieu

    The vertebrate clade diverged into Chondrichthyes (sharks, rays, and chimeras) and Osteichthyes fishes (bony fishes) approximately 420 mya, with each group accumulating vast anatomical and physiological differences, including skin properties. The skin of Chondrichthyes fishes is covered in dermal denticles, whereas Osteichthyes fishes are covered in scales and are mucous rich. The divergence time among

  • Climate mediates continental scale patterns of stream microbial functional diversity.
    Microbiome (IF 11.607) Pub Date : 2020-06-13
    Félix Picazo,Annika Vilmi,Juha Aalto,Janne Soininen,Emilio O Casamayor,Yongqin Liu,Qinglong Wu,Lijuan Ren,Jizhong Zhou,Ji Shen,Jianjun Wang

    Understanding the large-scale patterns of microbial functional diversity is essential for anticipating climate change impacts on ecosystems worldwide. However, studies of functional biogeography remain scarce for microorganisms, especially in freshwater ecosystems. Here we study 15,289 functional genes of stream biofilm microbes along three elevational gradients in Norway, Spain and China. We find

  • Topography of the respiratory tract bacterial microbiota in cattle.
    Microbiome (IF 11.607) Pub Date : 2020-06-10
    Christopher McMullen,Trevor W Alexander,Renaud Léguillette,Matthew Workentine,Edouard Timsit

    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

  • VIBRANT: automated recovery, annotation and curation of microbial viruses, and evaluation of viral community function from genomic sequences.
    Microbiome (IF 11.607) Pub Date : 2020-06-10
    Kristopher Kieft,Zhichao Zhou,Karthik Anantharaman

    Viruses are central to microbial community structure in all environments. The ability to generate large metagenomic assemblies of mixed microbial and viral sequences provides the opportunity to tease apart complex microbiome dynamics, but these analyses are currently limited by the tools available for analyses of viral genomes and assessing their metabolic impacts on microbiomes. Here we present VIBRANT

  • Depth-related variability in viral communities in highly stratified sulfidic mine tailings.
    Microbiome (IF 11.607) Pub Date : 2020-06-09
    Shao-Ming Gao,Axel Schippers,Nan Chen,Yang Yuan,Miao-Miao Zhang,Qi Li,Bin Liao,Wen-Sheng Shu,Li-Nan Huang

    Recent studies have significantly expanded our knowledge of viral diversity and functions in the environment. Exploring the ecological relationships between viruses, hosts, and the environment is a crucial first step towards a deeper understanding of the complex and dynamic interplays among them. Here, we obtained extensive 16S rRNA gene amplicon, metagenomics sequencing, and geochemical datasets from

  • Bacteroides thetaiotaomicron-derived outer membrane vesicles promote regulatory dendritic cell responses in health but not in inflammatory bowel disease.
    Microbiome (IF 11.607) Pub Date : 2020-06-08
    Lydia Durant,Régis Stentz,Alistair Noble,Johanne Brooks,Nadezhda Gicheva,Durga Reddi,Matthew J O'Connor,Lesley Hoyles,Anne L McCartney,Ripple Man,E Tobias Pring,Stella Dilke,Philip Hendy,Jonathan P Segal,Dennis N F Lim,Ravi Misra,Ailsa L Hart,Naila Arebi,Simon R Carding,Stella C Knight

    Bacteroides thetaiotaomicron (Bt) is a prominent member of the human intestinal microbiota that, like all gram-negative bacteria, naturally generates nanosized outer membrane vesicles (OMVs) which bud off from the cell surface. Importantly, OMVs can cross the intestinal epithelial barrier to mediate microbe-host cell crosstalk involving both epithelial and immune cells to help maintain intestinal homeostasis

  • Re-evaluating the relationship between missing heritability and the microbiome.
    Microbiome (IF 11.607) Pub Date : 2020-06-08
    Gavin M Douglas,Joseph P Bielawski,Morgan G I Langille

    Human genome-wide association studies (GWASs) have recurrently estimated lower heritability estimates than familial studies. Many explanations have been suggested to explain these lower estimates, including that a substantial proportion of genetic variation and gene-by-environment interactions are unmeasured in typical GWASs. The human microbiome is potentially related to both of these explanations

  • Temporal variations in bacterial community diversity and composition throughout intensive care unit renovations.
    Microbiome (IF 11.607) Pub Date : 2020-06-08
    Jessica Chopyk,Kevan Akrami,Tovia Bavly,Ji H Shin,Leila K Schwanemann,Melissa Ly,Richa Kalia,Ying Xu,Scott T Kelley,Atul Malhotra,Francesca J Torriani,Daniel A Sweeney,David T Pride

    Inanimate surfaces within a hospital serve as a reservoir of microbial life that may colonize patients and ultimately result in healthcare associated infections (HAIs). Critically ill patients in intensive care units (ICUs) are particularly vulnerable to HAIs. Little is known about how the microbiome of the ICU is established or what factors influence its evolution over time. A unique opportunity to

  • Skin microbiota analysis-inspired development of novel anti-infectives.
    Microbiome (IF 11.607) Pub Date : 2020-06-05
    Yao Liu,Yuanzhen Liu,Zixiu Du,Lidan Zhang,Juan Chen,Zhen Shen,Qian Liu,Juanxiu Qin,Huiying Lv,Hua Wang,Lei He,Junlan Liu,Qian Huang,Yuhui Sun,Michael Otto,Min Li

    The alarming spread of antimicrobial resistance requires the development of novel anti-infective drugs. Despite the recent research focus on the human microbiome and its likely value to understand and exploit inter-bacterial inhibitory phenomena as a source for antimicrobial strategies, the human microbiota has barely been investigated for the purpose of drug development. We performed a large screen

  • Winter warming in Alaska accelerates lignin decomposition contributed by Proteobacteria.
    Microbiome (IF 11.607) Pub Date : 2020-06-05
    Xuanyu Tao,Jiajie Feng,Yunfeng Yang,Gangsheng Wang,Renmao Tian,Fenliang Fan,Daliang Ning,Colin T Bates,Lauren Hale,Mengting M Yuan,Linwei Wu,Qun Gao,Jiesi Lei,Edward A G Schuur,Julian Yu,Rosvel Bracho,Yiqi Luo,Konstantinos T Konstantinidis,Eric R Johnston,James R Cole,C Ryan Penton,James M Tiedje,Jizhong Zhou

    In a warmer world, microbial decomposition of previously frozen organic carbon (C) is one of the most likely positive climate feedbacks of permafrost regions to the atmosphere. However, mechanistic understanding of microbial mediation on chemically recalcitrant C instability is limited; thus, it is crucial to identify and evaluate active decomposers of chemically recalcitrant C, which is essential

  • Mechanistic insights into the attenuation of intestinal inflammation and modulation of the gut microbiome by krill oil using in vitro and in vivo models.
    Microbiome (IF 11.607) Pub Date : 2020-06-04
    Fang Liu,Allen D Smith,Gloria Solano-Aguilar,Thomas T Y Wang,Quynhchi Pham,Ethiopia Beshah,Qingjuan Tang,Joseph F Urban,Changhu Xue,Robert W Li

    The anti-inflammatory property of ω-3 polyunsaturated fatty acids (PUFA) has been exploited in the management of inflammatory bowel disease (IBD) with promising results. However, it remains unclear if PUFA play a significant role in the resolution of inflammation and promotion of mucosal healing. Krill oil (KO) is a natural product rich in PUFA and the potent antioxidant, astaxanthin. In this study

  • Earth microbial co-occurrence network reveals interconnection pattern across microbiomes.
    Microbiome (IF 11.607) Pub Date : 2020-06-04
    Bin Ma,Yiling Wang,Shudi Ye,Shan Liu,Erinne Stirling,Jack A Gilbert,Karoline Faust,Rob Knight,Janet K Jansson,Cesar Cardona,Lisa Röttjers,Jianming Xu

    Microbial interactions shape the structure and function of microbial communities; microbial co-occurrence networks in specific environments have been widely developed to explore these complex systems, but their interconnection pattern across microbiomes in various environments at the global scale remains unexplored. Here, we have inferred an Earth microbial co-occurrence network from a communal catalog

  • Diversity of isoprene-degrading bacteria in phyllosphere and soil communities from a high isoprene-emitting environment: a Malaysian oil palm plantation.
    Microbiome (IF 11.607) Pub Date : 2020-06-03
    Ornella Carrión,Lisa Gibson,Dafydd M O Elias,Niall P McNamara,Theo A van Alen,Huub J M Op den Camp,Christina Vimala Supramaniam,Terry J McGenity,J Colin Murrell

    Isoprene is the most abundantly produced biogenic volatile organic compound (BVOC) on Earth, with annual global emissions almost equal to those of methane. Despite its importance in atmospheric chemistry and climate, little is known about the biological degradation of isoprene in the environment. The largest source of isoprene is terrestrial plants, and oil palms, the cultivation of which is expanding

  • Engineering CRISPR/Cas9 to mitigate abundant host contamination for 16S rRNA gene-based amplicon sequencing.
    Microbiome (IF 11.607) Pub Date : 2020-06-03
    Luyang Song,Kabin Xie

    High-throughput sequencing of bacterial 16S rRNA gene (16S-seq) is a useful and common method for studying bacterial community structures. However, contamination of the 16S rRNA genes from the mitochondrion and plastid hinders the sensitive bacterial 16S-seq in plant microbiota profiling, especially for some plant species such as rice. To date, efficiently mitigating such host contamination without

  • Using soil bacterial communities to predict physico-chemical variables and soil quality.
    Microbiome (IF 11.607) Pub Date : 2020-06-02
    Syrie M Hermans,Hannah L Buckley,Bradley S Case,Fiona Curran-Cournane,Matthew Taylor,Gavin Lear

    Soil ecosystems consist of complex interactions between biological communities and physico-chemical variables, all of which contribute to the overall quality of soils. Despite this, changes in bacterial communities are ignored by most soil monitoring programs, which are crucial to ensure the sustainability of land management practices. We applied 16S rRNA gene sequencing to determine the bacterial