Articles

Spatial scale affects the relative role of stochasticity versus determinism in soil bacterial communities in wheat fields across the North China Plain

The relative importance of stochasticity versus determinism in soil bacterial communities is unclear, as are the possible influences that alter the balance between these. Here, we investigated the influence of...

Authors: Yu Shi, Yuntao Li, Xingjia Xiang, Ruibo Sun, Teng Yang, Dan He, Kaoping Zhang, Yingying Ni, Yong-Guan Zhu, Jonathan M. Adams and Haiyan Chu

Individual and household attributes influence the dynamics of the personal skin microbiota and its association network

Numerous studies have thus far characterized the temporal dynamics of the skin microbiota of healthy individuals. However, there is no information regarding the dynamics of different microbial association netw...

Authors: Marcus H. Y. Leung, Xinzhao Tong, David Wilkins, Hedwig H. L. Cheung and Patrick K. H. Lee

Crawling-induced floor dust resuspension affects the microbiota of the infant breathing zone

Floor dust is commonly used for microbial determinations in epidemiological studies to estimate early-life indoor microbial exposures. Resuspension of floor dust and its impact on infant microbial exposure is,...

Authors: Heidi K. Hyytiäinen, Balamuralikrishna Jayaprakash, Pirkka V. Kirjavainen, Sampo E. Saari, Rauno Holopainen, Jorma Keskinen, Kaarle Hämeri, Anne Hyvärinen, Brandon E. Boor and Martin Täubel

DeepARG: a deep learning approach for predicting antibiotic resistance genes from metagenomic data

Growing concerns about increasing rates of antibiotic resistance call for expanded and comprehensive global monitoring. Advancing methods for monitoring of environmental media (e.g., wastewater, agricultural w...

Authors: Gustavo Arango-Argoty, Emily Garner, Amy Pruden, Lenwood S. Heath, Peter Vikesland and Liqing Zhang

A human gut phage catalog correlates the gut phageome with type 2 diabetes

Substantial efforts have been made to link the gut bacterial community to many complex human diseases. Nevertheless, the gut phages are often neglected.

Authors: Yingfei Ma, Xiaoyan You, Guoqin Mai, Taku Tokuyasu and Chenli Liu

Integrated multi-omic analysis of host-microbiota interactions in acute oak decline

Britain’s native oak species are currently under threat from acute oak decline (AOD), a decline-disease where stem bleeds overlying necrotic lesions in the inner bark and larval galleries of the bark-boring be...

Authors: Martin Broberg, James Doonan, Filip Mundt, Sandra Denman and James E. McDonald

Filter forensics: microbiota recovery from residential HVAC filters

Establishing reliable methods for assessing the microbiome within the built environment is critical for understanding the impact of biological exposures on human health. High-throughput DNA sequencing of dust ...

Authors: Juan P. Maestre, Wiley Jennings, Dennis Wylie, Sharon D. Horner, Jeffrey Siegel and Kerry A. Kinney

Commensal microbiota modulate gene expression in the skin

The skin harbors complex communities of resident microorganisms, yet little is known of their physiological roles and the molecular mechanisms that mediate cutaneous host-microbe interactions. Here, we profile...

Authors: Jacquelyn S. Meisel, Georgia Sfyroera, Casey Bartow-McKenney, Ciara Gimblet, Julia Bugayev, Joseph Horwinski, Brian Kim, Jonathan R. Brestoff, Amanda S. Tyldsley, Qi Zheng, Brendan P. Hodkinson, David Artis and Elizabeth A. Grice

Metagenomic investigation of vestimentiferan tubeworm endosymbionts from Mid-Cayman Rise reveals new insights into metabolism and diversity

The microbial endosymbionts of two species of vestimentiferan tubeworms (Escarpia sp. and Lamellibrachia sp.2) collected from an area of low-temperature hydrothermal diffuse vent flow at the Mid-Cayman Rise (MCR)...

Authors: Julie Reveillaud, Rika Anderson, Sintra Reves-Sohn, Colleen Cavanaugh and Julie A. Huber

Apple endophytic microbiota of different rootstock/scion combinations suggests a genotype-specific influence

High-throughput amplicon sequencing spanning conserved portions of microbial genomes (16s rRNA and ITS) was used in the present study to describe the endophytic microbiota associated with three apple varieties...

Authors: Jia Liu, Ahmed Abdelfattah, John Norelli, Erik Burchard, Leonardo Schena, Samir Droby and Michael Wisniewski

Combining 16S rRNA gene variable regions enables high-resolution microbial community profiling

Most of our knowledge about the remarkable microbial diversity on Earth comes from sequencing the 16S rRNA gene. The use of next-generation sequencing methods has increased sample number and sequencing depth, ...

Authors: Garold Fuks, Michael Elgart, Amnon Amir, Amit Zeisel, Peter J. Turnbaugh, Yoav Soen and Noam Shental

Integrated biogeography of planktonic and sedimentary bacterial communities in the Yangtze River

Bacterial communities are essential to the biogeochemical cycle in riverine ecosystems. However, little is presently known about the integrated biogeography of planktonic and sedimentary bacterial communities ...

Authors: Tang Liu, An Ni Zhang, Jiawen Wang, Shufeng Liu, Xiaotao Jiang, Chenyuan Dang, Tao Ma, Sitong Liu, Qian Chen, Shuguang Xie, Tong Zhang and Jinren Ni

ReprDB and panDB: minimalist databases with maximal microbial representation

Profiling of shotgun metagenomic samples is hindered by a lack of unified microbial reference genome databases that (i) assemble genomic information from all open access microbial genomes, (ii) have relatively...

Authors: Wei Zhou, Nicole Gay and Julia Oh

Cropping practices manipulate abundance patterns of root and soil microbiome members paving the way to smart farming

Harnessing beneficial microbes presents a promising strategy to optimize plant growth and agricultural sustainability. Little is known to which extent and how specifically soil and plant microbiomes can be man...

Authors: Kyle Hartman, Marcel G. A. van der Heijden, Raphaël A. Wittwer, Samiran Banerjee, Jean-Claude Walser and Klaus Schlaeppi

Fungi stabilize connectivity in the lung and skin microbial ecosystems

No microbe exists in isolation, and few live in environments with only members of their own kingdom or domain. As microbiome studies become increasingly more interested in the interactions between microbes tha...

Authors: Laura Tipton, Christian L. Müller, Zachary D. Kurtz, Laurence Huang, Eric Kleerup, Alison Morris, Richard Bonneau and Elodie Ghedin

In-depth resistome analysis by targeted metagenomics

Antimicrobial resistance is a major global health challenge. Metagenomics allows analyzing the presence and dynamics of “resistomes” (the ensemble of genes encoding antimicrobial resistance in a given microbio...

Authors: Val F. Lanza, Fernando Baquero, José Luís Martínez, Ricardo Ramos-Ruíz, Bruno González-Zorn, Antoine Andremont, Antonio Sánchez-Valenzuela, Stanislav Dusko Ehrlich, Sean Kennedy, Etienne Ruppé, Willem van Schaik, Rob J. Willems, Fernando de la Cruz and Teresa M. Coque

Multi-omics differentially classify disease state and treatment outcome in pediatric Crohn’s disease

Crohn’s disease (CD) has an unclear etiology, but there is growing evidence of a direct link with a dysbiotic microbiome. Many gut microbes have previously been associated with CD, but these have mainly been c...

Authors: Gavin M. Douglas, Richard Hansen, Casey M. A. Jones, Katherine A. Dunn, André M. Comeau, Joseph P. Bielawski, Rachel Tayler, Emad M. El-Omar, Richard K. Russell, Georgina L. Hold, Morgan G. I. Langille and Johan Van Limbergen

Haemophilus is overrepresented in the nasopharynx of infants hospitalized with RSV infection and associated with increased viral load and enhanced mucosal CXCL8 responses

While almost all infants are infected with respiratory syncytial virus (RSV) before the age of 2 years, only a small percentage develops severe disease. Previous studies suggest that the nasopharyngeal microbi...

Authors: Thomas H. A. Ederveen, Gerben Ferwerda, Inge M. Ahout, Marloes Vissers, Ronald de Groot, Jos Boekhorst, Harro M. Timmerman, Martijn A. Huynen, Sacha A. F. T. van Hijum and Marien I. de Jonge

Influenza A virus infection impacts systemic microbiota dynamics and causes quantitative enteric dysbiosis

Microbiota integrity is essential for a growing number of physiological processes. Consequently, disruption of microbiota homeostasis correlates with a variety of pathological states. Importantly, commensal mi...

Authors: Soner Yildiz, Béryl Mazel-Sanchez, Matheswaran Kandasamy, Balaji Manicassamy and Mirco Schmolke

“Available upon request”: not good enough for microbiome data!

Authors: Morgan G. I. Langille, Jacques Ravel and W. Florian Fricke

The lung tissue microbiota of mild and moderate chronic obstructive pulmonary disease

Oral taxa are often found in the chronic obstructive pulmonary disease (COPD) lung microbiota, but it is not clear if this is due to a physiologic process such as aspiration or experimental contamination at th...

Authors: Alexa A. Pragman, Tianmeng Lyu, Joshua A. Baller, Trevor J. Gould, Rosemary F. Kelly, Cavan S. Reilly, Richard E. Isaacson and Chris H. Wendt

An IMD-like pathway mediates both endosymbiont control and host immunity in the cereal weevil Sitophilus spp.

Many insects developing on nutritionally unbalanced diets have evolved symbiotic associations with vertically transmitted intracellular bacteria (endosymbionts) that provide them with metabolic components, the...

Authors: Justin Maire, Carole Vincent-Monégat, Florent Masson, Anna Zaidman-Rémy and Abdelaziz Heddi

Metabolic capability and in situ activity of microorganisms in an oil reservoir

Microorganisms have long been associated with oxic and anoxic degradation of hydrocarbons in oil reservoirs and oil production facilities. While we can readily determine the abundance of microorganisms in the ...

Authors: Yi-Fan Liu, Daniela Domingos Galzerani, Serge Maurice Mbadinga, Livia S. Zaramela, Ji-Dong Gu, Bo-Zhong Mu and Karsten Zengler

Host contributes to longitudinal diversity of fecal microbiota in swine selected for lean growth

In pigs, gut bacteria have been shown to play important roles in nutritional, physiological, and immunological processes in the host. However, the contribution of their metagenomes or part of them, which are n...

Authors: Duc Lu, Francesco Tiezzi, Constantino Schillebeeckx, Nathan P. McNulty, Clint Schwab, Caleb Shull and Christian Maltecca

Grapevine rootstocks shape underground bacterial microbiome and networking but not potential functionality

The plant compartments of Vitis vinifera, including the rhizosphere, rhizoplane, root endosphere, phyllosphere and carposphere, provide unique niches that drive specific bacterial microbiome associations. The maj...

Authors: Ramona Marasco, Eleonora Rolli, Marco Fusi, Grégoire Michoud and Daniele Daffonchio

The association between anterior nares and nasopharyngeal microbiota in infants hospitalized for bronchiolitis

The airway microbiome is a subject of great interest for the study of respiratory disease. Anterior nare samples are more accessible than samples from deeper within the nasopharynx. However, the correlation be...

Authors: Pamela N. Luna, Kohei Hasegawa, Nadim J. Ajami, Janice A. Espinola, David M. Henke, Joseph F. Petrosino, Pedro A. Piedra, Ashley F. Sullivan, Carlos A. Camargo Jr., Chad A. Shaw and Jonathan M. Mansbach

Aerobic proteobacterial methylotrophs in Movile Cave: genomic and metagenomic analyses

Movile Cave (Mangalia, Romania) is a unique ecosystem where the food web is sustained by microbial primary production, analogous to deep-sea hydrothermal vents. Specifically, chemoautotrophic microbes deriving...

Authors: Deepak Kumaresan, Jason Stephenson, Andrew C. Doxey, Hina Bandukwala, Elliot Brooks, Alexandra Hillebrand-Voiculescu, Andrew S. Whiteley and J Colin Murrell

Under control: how a dietary additive can restore the gut microbiome and proteomic profile, and improve disease resilience in a marine teleostean fish fed vegetable diets

The constant increase of aquaculture production and wealthy seafood consumption has forced the industry to explore alternative and more sustainable raw aquafeed materials, and plant ingredients have been used ...

Authors: María Carla Piazzon, Josep Alvar Calduch-Giner, Belén Fouz, Itziar Estensoro, Paula Simó-Mirabet, Mónica Puyalto, Vasileios Karalazos, Oswaldo Palenzuela, Ariadna Sitjà-Bobadilla and Jaume Pérez-Sánchez

Wild eel microbiome reveals that skin mucus of fish could be a natural niche for aquatic mucosal pathogen evolution

Fish skin mucosal surfaces (SMS) are quite similar in composition and function to some mammalian MS and, in consequence, could constitute an adequate niche for the evolution of mucosal aquatic pathogens in nat...

Authors: Miguel Carda-Diéguez, Rohit Ghai, Francisco Rodríguez-Valera and Carmen Amaro

Seasonal, spatial, and maternal effects on gut microbiome in wild red squirrels

Our understanding of gut microbiota has been limited primarily to findings from human and laboratory animals, but what shapes the gut microbiota in nature remains largely unknown. To fill this gap, we conducte...

Authors: Tiantian Ren, Stan Boutin, Murray M. Humphries, Ben Dantzer, Jamieson C. Gorrell, David W. Coltman, Andrew G. McAdam and Martin Wu

Quinones are growth factors for the human gut microbiota

The human gut microbiome has been linked to numerous components of health and disease. However, approximately 25% of the bacterial species in the gut remain uncultured, which limits our ability to properly und...

Authors: Kathrin Fenn, Philip Strandwitz, Eric J. Stewart, Eric Dimise, Sarah Rubin, Shreya Gurubacharya, Jon Clardy and Kim Lewis

Discovery of the fourth mobile sulfonamide resistance gene

Over the past 75 years, human pathogens have acquired antibiotic resistance genes (ARGs), often from environmental bacteria. Integrons play a major role in the acquisition of antibiotic resistance genes. We th...

Authors: Mohammad Razavi, Nachiket P. Marathe, Michael R. Gillings, Carl-Fredrik Flach, Erik Kristiansson and D. G. Joakim Larsson

Impact of prematurity and nutrition on the developing gut microbiome and preterm infant growth

Identification of factors that influence the neonatal gut microbiome is urgently needed to guide clinical practices that support growth of healthy preterm infants. Here, we examined the influence of nutrition ...

Authors: Alex Grier, Xing Qiu, Sanjukta Bandyopadhyay, Jeanne Holden-Wiltse, Haeja A. Kessler, Ann L. Gill, Brooke Hamilton, Heidie Huyck, Sara Misra, Thomas J. Mariani, Rita M. Ryan, Lori Scholer, Kristin M. Scheible, Yi-Horng Lee, Mary T. Caserta, Gloria S. Pryhuber…

The rumen microbiome as a reservoir of antimicrobial resistance and pathogenicity genes is directly affected by diet in beef cattle

The emergence and spread of antimicrobial resistance is the most urgent current threat to human and animal health. An improved understanding of the abundance of antimicrobial resistance genes and genes associa...

Authors: Marc D. Auffret, Richard J. Dewhurst, Carol-Anne Duthie, John A. Rooke, R. John Wallace, Tom C. Freeman, Robert Stewart, Mick Watson and Rainer Roehe

MetaLab: an automated pipeline for metaproteomic data analysis

Research involving microbial ecosystems has drawn increasing attention in recent years. Studying microbe-microbe, host-microbe, and environment-microbe interactions are essential for the understanding of micro...

Authors: Kai Cheng, Zhibin Ning, Xu Zhang, Leyuan Li, Bo Liao, Janice Mayne, Alain Stintzi and Daniel Figeys

Multi-level comparisons of cloacal, skin, feather and nest-associated microbiota suggest considerable influence of horizontal acquisition on the microbiota assembly of sympatric woodlarks and skylarks

Working toward a general framework to understand the role of microbiota in animal biology requires the characterisation of animal-associated microbial communities and identification of the evolutionary and eco...

Authors: H. Pieter J. van Veelen, Joana Falcao Salles and B. Irene Tieleman

Dietary energy drives the dynamic response of bovine rumen viral communities

Rumen microbes play a greater role in host energy acquisition than that of gut-associated microbes in monogastric animals. Although genome-enabled advancements are providing access to the vast diversity of unc...

Authors: Christopher L. Anderson, Matthew B. Sullivan and Samodha C. Fernando

Catalogue of antibiotic resistome and host-tracking in drinking water deciphered by a large scale survey

Excesses of antibiotic resistance genes (ARGs), which are regarded as emerging environmental pollutants, have been observed in various environments. The incidence of ARGs in drinking water causes potential ris...

Authors: Liping Ma, Bing Li, Xiao-Tao Jiang, Yu-Lin Wang, Yu Xia, An-Dong Li and Tong Zhang

The gut mycobiome of the Human Microbiome Project healthy cohort

Most studies describing the human gut microbiome in healthy and diseased states have emphasized the bacterial component, but the fungal microbiome (i.e., the mycobiome) is beginning to gain recognition as a fu...

Authors: Andrea K. Nash, Thomas A. Auchtung, Matthew C. Wong, Daniel P. Smith, Jonathan R. Gesell, Matthew C. Ross, Christopher J. Stewart, Ginger A. Metcalf, Donna M. Muzny, Richard A. Gibbs, Nadim J. Ajami and Joseph F. Petrosino

Characterization of the upper and lower respiratory tract microbiota in Piedmontese calves

The microbiota of the bovine upper respiratory tract has been recently characterized, but no data for the lower respiratory tract are available. A major health problem in bovine medicine is infectious bronchop...

Authors: Isabella Nicola, Francesco Cerutti, Elena Grego, Iride Bertone, Paola Gianella, Antonio D’Angelo, Simone Peletto and Claudio Bellino

Normalization of the microbiota in patients after treatment for colonic lesions

Colorectal cancer is a worldwide health problem. Despite growing evidence that members of the gut microbiota can drive tumorigenesis, little is known about what happens to it after treatment for an adenoma or ...

Authors: Marc A. Sze, Nielson T. Baxter, Mack T. Ruffin IV, Mary A. M. Rogers and Patrick D. Schloss

The Inuit gut microbiome is dynamic over time and shaped by traditional foods

The human gut microbiome represents a diverse microbial community that varies across individuals and populations, and is influenced by factors such as host genetics and lifestyle. Diet is a major force shaping...

Authors: Geneviève Dubois, Catherine Girard, François-Joseph Lapointe and B. Jesse Shapiro

Correction to: Towards a balanced view of the bacterial tree of life

Following publication of the original article [1], the authors pointed out that the figure shown as figure S1 is actually figure S2 and vice versa. Figure S1 should show the barcharts, and figure S2 should sho...

Authors: Frederik Schulz, Emiley A. Eloe-Fadrosh, Robert M. Bowers, Jessica Jarett, Torben Nielsen, Natalia N. Ivanova, Nikos C. Kyrpides and Tanja Woyke

Identifying predictive features of Clostridium difficile infection recurrence before, during, and after primary antibiotic treatment

Colonization by the pathogen Clostridium difficile often occurs in the background of a disrupted microbial community. Identifying specific organisms conferring resistance to invasion by C. difficile is desirable ...

Authors: Sepideh Pakpour, Amit Bhanvadia, Roger Zhu, Abhimanyu Amarnani, Sean M. Gibbons, Thomas Gurry, Eric J. Alm and Laura A. Martello

Pancreatic cyst fluid harbors a unique microbiome

It is clear that specific intestinal bacteria are involved in the development of different premalignant conditions along the gastrointestinal tract. An analysis of the microbial constituents in the context of ...

Authors: Shan Li, Gwenny M. Fuhler, Nahush BN, Tony Jose, Marco J. Bruno, Maikel P. Peppelenbosch and Sergey R. Konstantinov

Morphological and genetic factors shape the microbiome of a seabird species (Oceanodroma leucorhoa) more than environmental and social factors

The microbiome provides multiple benefits to animal hosts that can profoundly impact health and behavior. Microbiomes are well-characterized in humans and other animals in controlled settings, yet assessments ...

Authors: Douglas S. Pearce, Brian A. Hoover, Sarah Jennings, Gabrielle A. Nevitt and Kathryn M. Docherty

Dietary changes in nutritional studies shape the structural and functional composition of the pigs’ fecal microbiome—from days to weeks

The possible impact of changes in diet composition on the intestinal microbiome is mostly studied after some days of adaptation to the diet of interest. The question arises if a few days are enough to reflect ...

Authors: Bruno Tilocca, Katharina Burbach, Charlotte M. E. Heyer, Ludwig E. Hoelzle, Rainer Mosenthin, Volker Stefanski, Amélia Camarinha-Silva and Jana Seifert

Comparing microbiotas in the upper aerodigestive and lower respiratory tracts of lambs

Recently, the importance of the lung microbiota during health and disease has been examined in humans and in small animal models. Whilst sheep have been proposed as an appropriate large animal model for studyi...

Authors: Laura Glendinning, David Collie, Steven Wright, Kenny M. D. Rutherford and Gerry McLachlan

Microbial biodiversity assessment of the European Space Agency’s ExoMars 2016 mission

The ExoMars 2016 mission, consisting of the Trace Gas Orbiter and the Schiaparelli lander, was launched on March 14 2016 from Baikonur, Kazakhstan and reached its destination in October 2016. The Schiaparelli ...

Authors: Kaisa Koskinen, Petra Rettberg, Rüdiger Pukall, Anna Auerbach, Lisa Wink, Simon Barczyk, Alexandra Perras, Alexander Mahnert, Diana Margheritis, Gerhard Kminek and Christine Moissl-Eichinger

Towards a balanced view of the bacterial tree of life

The bacterial tree of life has recently undergone significant expansion, chiefly from candidate phyla retrieved through genome-resolved metagenomics. Bypassing the need for genome availability, we present a sn...

Authors: Frederik Schulz, Emiley A. Eloe-Fadrosh, Robert M. Bowers, Jessica Jarett, Torben Nielsen, Natalia N. Ivanova, Nikos C. Kyrpides and Tanja Woyke