Articles

Soil microbiomes with distinct assemblies through vertical soil profiles drive the cycling of multiple nutrients in reforested ecosystems

Soil microbiomes play an important role in the services and functioning of terrestrial ecosystems. However, little is known of their vertical responses to restoration process and their contributions to soil nu...

Authors: Shuo Jiao, Weimin Chen, Jieli Wang, Nini Du, Qiaoping Li and Gehong Wei

Tracing mother-infant transmission of bacteriophages by means of a novel analytical tool for shotgun metagenomic datasets: METAnnotatorX

Despite the relevance of viral populations, our knowledge of (bacterio) phage populations, i.e., the phageome, suffers from the absence of a “gold standard” protocol for viral DNA extraction with associated in...

Authors: Christian Milani, Eoghan Casey, Gabriele Andrea Lugli, Rebecca Moore, Joanna Kaczorowska, Conor Feehily, Marta Mangifesta, Leonardo Mancabelli, Sabrina Duranti, Francesca Turroni, Francesca Bottacini, Jennifer Mahony, Paul D. Cotter, Fionnuala M. McAuliffe, Douwe van Sinderen and Marco Ventura

Chloroplast sequence variation and the efficacy of peptide nucleic acids for blocking host amplification in plant microbiome studies

The ability to efficiently characterize microbial communities from host individuals can be limited by co-amplification of host organellar sequences (mitochondrial and/or plastid), which share a common ancestor...

Authors: Connor R. Fitzpatrick, Patricia Lu-Irving, Julia Copeland, David S. Guttman, Pauline W. Wang, David A. Baltrus, Katrina M. Dlugosch and Marc T. J. Johnson

The wild side of plant microbiomes

Authors: Juan E. Pérez-Jaramillo, Víctor J. Carrión, Mattias de Hollander and Jos M. Raaijmakers

Resilience of the resident soil microbiome to organic and inorganic amendment disturbances and to temporary bacterial invasion

Vinasse, a by-product of sugarcane ethanol production, is recycled by sugarcane plantations as a fertilizer due to its rich nutrient content. However, the impacts of the chemical and microbial composition of v...

Authors: Késia Silva Lourenço, Afnan K. A. Suleiman, A. Pijl, J. A. van Veen, H. Cantarella and E. E. Kuramae

The tick endosymbiont Candidatus Midichloria mitochondrii and selenoproteins are essential for the growth of Rickettsia parkeri in the Gulf Coast tick vector

Pathogen colonization inside tick tissues is a significant aspect of the overall competence of a vector. Amblyomma maculatum is a competent vector of the spotted fever group rickettsiae, Rickettsia parkeri. When

Authors: Khemraj Budachetri, Deepak Kumar, Gary Crispell, Christine Beck, Gregory Dasch and Shahid Karim

IDTAXA: a novel approach for accurate taxonomic classification of microbiome sequences

Microbiome studies often involve sequencing a marker gene to identify the microorganisms in samples of interest. Sequence classification is a critical component of this process, whereby sequences are assigned ...

Authors: Adithya Murali, Aniruddha Bhargava and Erik S. Wright

Trichoderma polysporum selectively inhibits white-nose syndrome fungal pathogen Pseudogymnoascus destructans amidst soil microbes

Pseudogymnoascus destructans (Pd), the causative fungal agent of white-nose syndrome (WNS), has led to the deaths of millions of hibernating bats in the United States of America (USA) and Canada. Efficient strate...

Authors: Amanpreet Singh, Erica Lasek-Nesselquist, Vishnu Chaturvedi and Sudha Chaturvedi

Viral and metabolic controls on high rates of microbial sulfur and carbon cycling in wetland ecosystems

Microorganisms drive high rates of methanogenesis and carbon mineralization in wetland ecosystems. These signals are especially pronounced in the Prairie Pothole Region of North America, the tenth largest wetl...

Authors: Paula Dalcin Martins, Robert E. Danczak, Simon Roux, Jeroen Frank, Mikayla A. Borton, Richard A. Wolfe, Marie N. Burris and Michael J. Wilkins

CLOUD: a non-parametric detection test for microbiome outliers

Dysbiosis of the human gut microbiome is defined as a maladaptive or clinically relevant deviation of the community profile from the healthy or normal state. Dysbiosis has been implicated in an extensive set o...

Authors: Emmanuel Montassier, Gabriel A. Al-Ghalith, Benjamin Hillmann, Kimberly Viskocil, Amanda J. Kabage, Christopher E. McKinlay, Michael J. Sadowsky, Alexander Khoruts and Dan Knights

Breast cancer in postmenopausal women is associated with an altered gut metagenome

Increasing evidence suggests that gut microbiota play a role in the pathogenesis of breast cancer. The composition and functional capacity of gut microbiota associated with breast cancer have not been studied ...

Authors: Jia Zhu, Ming Liao, Ziting Yao, Wenying Liang, Qibin Li, Jianlun Liu, Huawei Yang, Yinan Ji, Wei Wei, Aihua Tan, Siyuan Liang, Yang Chen, Haisong Lin, Xiujuan Zhu, Shengzhu Huang, Jiarong Tian…

A metagenomic study of the gut microbiome in Behcet’s disease

Behcet’s disease (BD) is a recalcitrant, multisystemic inflammatory disease that can lead to irreversible blindness. Microbial agents have been considered to contribute to the pathogenesis of this disease, but...

Authors: Zi Ye, Ni Zhang, Chunyan Wu, Xinyuan Zhang, Qingfeng Wang, Xinyue Huang, Liping Du, Qingfeng Cao, Jihong Tang, Chunjiang Zhou, Shengping Hou, Yue He, Qian Xu, Xiao Xiong, Aize Kijlstra, Nan Qin…

The gut microbiota drives the impact of bile acids and fat source in diet on mouse metabolism

As the gut microbiota contributes to metabolic health, it is important to determine specific diet-microbiota interactions that influence host metabolism. Bile acids and dietary fat source can alter phenotypes ...

Authors: Sarah Just, Stanislas Mondot, Josef Ecker, Katrin Wegner, Eva Rath, Laura Gau, Theresa Streidl, Genevieve Hery-Arnaud, Sinah Schmidt, Till Robin Lesker, Valentin Bieth, Andreas Dunkel, Till Strowig, Thomas Hofmann, Dirk Haller, Gerhard Liebisch…

A prebiotic intervention study in children with autism spectrum disorders (ASDs)

Different dietary approaches, such as gluten and casein free diets, or the use of probiotics and prebiotics have been suggested in autistic spectrum disorders in order to reduce gastrointestinal (GI) disturban...

Authors: Roberta Grimaldi, Glenn R. Gibson, Jelena Vulevic, Natasa Giallourou, Josué L. Castro-Mejía, Lars H. Hansen, E. Leigh Gibson, Dennis S. Nielsen and Adele Costabile

Bacterial microbiota protect an invasive bark beetle from a pine defensive compound

There is growing evidence that some devastating biotic invasions are facilitated by microbial symbionts. The red turpentine beetle (RTB), an innocuous secondary insect attacking weakened trees in North America...

Authors: Chihang Cheng, Jacob D Wickham, Li Chen, Dandan Xu, Min Lu and Jianghua Sun

A two-stage microbial association mapping framework with advanced FDR control

In microbiome studies, it is important to detect taxa which are associated with pathological outcomes at the lowest definable taxonomic rank, such as genus or species. Traditionally, taxa at the target rank ar...

Authors: Jiyuan Hu, Hyunwook Koh, Linchen He, Menghan Liu, Martin J. Blaser and Huilin Li

Conserved phylogenetic distribution and limited antibiotic resistance of class 1 integrons revealed by assessing the bacterial genome and plasmid collection

Integrons, especially the class 1 integrons, are major contributors to the acquisition and dissemination of antibiotic resistance genes (ARGs). However, comprehensive knowledge of the types, content, and distr...

Authors: An Ni Zhang, Li-Guan Li, Liping Ma, Michael R. Gillings, James M. Tiedje and Tong Zhang

The evolutionary signal in metagenome phyletic profiles predicts many gene functions

The function of many genes is still not known even in model organisms. An increasing availability of microbiome DNA sequencing data provides an opportunity to infer gene function in a systematic manner.

Authors: Vedrana Vidulin, Tomislav Šmuc, Sašo Džeroski and Fran Supek

Fine metagenomic profile of the Mediterranean stratified and mixed water columns revealed by assembly and recruitment

The photic zone of aquatic habitats is subjected to strong physicochemical gradients. To analyze the fine-scale variations in the marine microbiome, we collected seven samples from a single offshore location i...

Authors: Jose M. Haro-Moreno, Mario López-Pérez, José R. de la Torre, Antonio Picazo, Antonio Camacho and Francisco Rodriguez-Valera

Correction to: Metagenomics of urban sewage identifies an extensively shared antibiotic resistome in China

Unfortunately, after publication of this article [1], it was noticed that the accession numbers for the study were missing. The correct numbers are PRJNA438554, SRP148953.

Authors: Jian-Qiang Su, Xin-Li An, Bing Li, Qing-Lin Chen, Michael R. Gillings, Hong Chen, Tong Zhang and Yong-Guan Zhu

Correction to: Huddling remodels gut microbiota to reduce energy requirements in a small mammal species during cold exposure

Following publication of the original article [1], the authors reported an error in the caption of Fig. 4.

Authors: Xue-Ying Zhang, Gansukh Sukhchuluun, Ting-Bei Bo, Qing-Sheng Chi, Jun-Jie Yang, Bin Chen, Lei Zhang and De-Hua Wang

The diversity of uncharacterized antibiotic resistance genes can be predicted from known gene variants—but not always

Antibiotic resistance is considered one of the most urgent threats to modern healthcare, and the role of the environment in resistance development is increasingly recognized. It is often assumed that the abund...

Authors: Johan Bengtsson-Palme

Disruption of maternal gut microbiota during gestation alters offspring microbiota and immunity

Early life microbiota is an important determinant of immune and metabolic development and may have lasting consequences. The maternal gut microbiota during pregnancy or breastfeeding is important for defining ...

Authors: Donald D. Nyangahu, Katie S. Lennard, Bryan P. Brown, Matthew G. Darby, Jerome M. Wendoh, Enock Havyarimana, Peter Smith, James Butcher, Alain Stintzi, Nicola Mulder, William Horsnell and Heather B. Jaspan

Metagenomic analysis of basal ice from an Alaskan glacier

Glaciers cover ~ 10% of land but are among the least explored environments on Earth. The basal portion of glaciers often harbors unique aquatic microbial ecosystems in the absence of sunlight, and knowledge on...

Authors: Masood ur Rehman Kayani, Shawn M. Doyle, Naseer Sangwan, Guanqun Wang, Jack A. Gilbert, Brent C. Christner and Ting F. Zhu

Maternal diet during pregnancy is related with the infant stool microbiome in a delivery mode-dependent manner

The gut microbiome has an important role in infant health and immune development and may be affected by early-life exposures. Maternal diet may influence the infant gut microbiome through vertical transfer of ...

Authors: Sara N. Lundgren, Juliette C. Madan, Jennifer A. Emond, Hilary G. Morrison, Brock C. Christensen, Margaret R. Karagas and Anne G. Hoen

Stable isotope informed genome-resolved metagenomics reveals that Saccharibacteria utilize microbially-processed plant-derived carbon

The transformation of plant photosynthate into soil organic carbon and its recycling to CO₂ by soil microorganisms is one of the central components of the terrestrial carbon cycle. There are currently large knowl...

Authors: Evan P. Starr, Shengjing Shi, Steven J. Blazewicz, Alexander J. Probst, Donald J. Herman, Mary K. Firestone and Jillian F. Banfield

Probiotic Bifidobacterium strains and galactooligosaccharides improve intestinal barrier function in obese adults but show no synergism when used together as synbiotics

One way to improve both the ecological performance and functionality of probiotic bacteria is by combining them with a prebiotic in the form of a synbiotic. However, the degree to which such synbiotic formulat...

Authors: Janina A. Krumbeck, Heather E. Rasmussen, Robert W. Hutkins, Jennifer Clarke, Krista Shawron, Ali Keshavarzian and Jens Walter

Signatures of ecological processes in microbial community time series

Growth rates, interactions between community members, stochasticity, and immigration are important drivers of microbial community dynamics. In sequencing data analysis, such as network construction and communi...

Authors: Karoline Faust, Franziska Bauchinger, Béatrice Laroche, Sophie de Buyl, Leo Lahti, Alex D. Washburne, Didier Gonze and Stefanie Widder

Evaluation of bias induced by viral enrichment and random amplification protocols in metagenomic surveys of saliva DNA viruses

Viruses are key players regulating microbial ecosystems. Exploration of viral assemblages is now possible thanks to the development of metagenomics, the most powerful tool available for studying viral ecology ...

Authors: Marcos Parras-Moltó, Ana Rodríguez-Galet, Patricia Suárez-Rodríguez and Alberto López-Bueno

Facultative methanotrophs are abundant at terrestrial natural gas seeps

Natural gas contains methane and the gaseous alkanes ethane, propane and butane, which collectively influence atmospheric chemistry and cause global warming. Methane-oxidising bacteria, methanotrophs, are cruc...

Authors: Muhammad Farhan Ul Haque, Andrew T. Crombie, Scott A. Ensminger, Calin Baciu and J. Colin Murrell

Increased richness and diversity of the vaginal microbiota and spontaneous preterm birth

The bacterial community present in the female lower genital tract plays an important role in maternal and neonatal health. Imbalances in this microbiota have been associated with negative reproductive outcomes...

Authors: Aline C. Freitas, Alan Bocking, Janet E. Hill and Deborah M. Money

Network hubs in root-associated fungal metacommunities

Although a number of recent studies have uncovered remarkable diversity of microbes associated with plants, understanding and managing dynamics of plant microbiomes remain major scientific challenges. In this ...

Authors: Hirokazu Toju, Akifumi S. Tanabe and Hirotoshi Sato

Microbial diversity and community composition of caecal microbiota in commercial and indigenous Indian chickens determined using 16s rDNA amplicon sequencing

The caecal microbiota plays a key role in chicken health and performance, influencing digestion and absorption of nutrients, and contributing to defence against colonisation by invading pathogens. Measures of ...

Authors: Ramesh J. Pandit, Ankit T. Hinsu, Namrata V. Patel, Prakash G. Koringa, Subhash J. Jakhesara, Jalpa R. Thakkar, Tejas M. Shah, Georgina Limon, Androniki Psifidi, Javier Guitian, David A. Hume, Fiona M. Tomley, Dharamshibhai N. Rank, M. Raman, K. G. Tirumurugaan, Damer P. Blake…

1-Aminocyclopropane-1-carboxylate deaminase producers associated to maize and other Poaceae species

Complex plant-microbe interactions have been established throughout evolutionary time, many of them with beneficial effects on the host in terms of plant growth, nutrition, or health. Some of the corresponding...

Authors: Marie-Lara Bouffaud, Sébastien Renoud, Audrey Dubost, Yvan Moënne-Loccoz and Daniel Muller

Genomic variation and biogeography of Antarctic haloarchaea

The genomes of halophilic archaea (haloarchaea) often comprise multiple replicons. Genomic variation in haloarchaea has been linked to viral infection pressure and, in the case of Antarctic communities, can be...

Authors: Bernhard Tschitschko, Susanne Erdmann, Matthew Z. DeMaere, Simon Roux, Pratibha Panwar, Michelle A. Allen, Timothy J. Williams, Sarah Brazendale, Alyce M. Hancock, Emiley A. Eloe-Fadrosh and Ricardo Cavicchioli

The developing premature infant gut microbiome is a major factor shaping the microbiome of neonatal intensive care unit rooms

The neonatal intensive care unit (NICU) contains a unique cohort of patients with underdeveloped immune systems and nascent microbiome communities. Patients often spend several months in the same room, and it ...

Authors: Brandon Brooks, Matthew R. Olm, Brian A. Firek, Robyn Baker, David Geller-McGrath, Sophia R. Reimer, Karina R. Soenjoyo, Jennifer S. Yip, Dylan Dahan, Brian C. Thomas, Michael J. Morowitz and Jillian F. Banfield

Metabolomic signatures distinguish the impact of formula carbohydrates on disease outcome in a preterm piglet model of NEC

Major risk factors for necrotizing enterocolitis (NEC) include premature birth and formula feeding in the context of microbial colonization of the gastrointestinal tract. We previously showed that feeding form...

Authors: Lee Call, Barbara Stoll, Berthe Oosterloo, Nadim Ajami, Fariha Sheikh, Anja Wittke, Rosaline Waworuntu, Brian Berg, Joseph Petrosino, Oluyinka Olutoye and Douglas Burrin

Absolute quantitation of microbiota abundance in environmental samples

Microbial communities (microbiota) influence human and animal disease and immunity, geochemical nutrient cycling and plant productivity. Specific groups, including bacteria, archaea, eukaryotes or fungi, are a...

Authors: Andrzej Tkacz, Marion Hortala and Philip S. Poole

The queen’s gut refines with age: longevity phenotypes in a social insect model

In social insects, identical genotypes can show extreme lifespan variation providing a unique perspective on age-associated microbial succession. In honey bees, short- and long-lived host phenotypes are polari...

Authors: Kirk E. Anderson, Vincent A. Ricigliano, Brendon M. Mott, Duan C. Copeland, Amy S. Floyd and Patrick Maes

Saturated long-chain fatty acid-producing bacteria contribute to enhanced colonic motility in rats

The gut microbiota is closely associated with gastrointestinal (GI) motility disorder, but the mechanism(s) by which bacteria interact with and affect host GI motility remains unclear. In this study, through u...

Authors: Ling Zhao, Yufen Huang, Lin Lu, Wei Yang, Tao Huang, Zesi Lin, Chengyuan Lin, Hiuyee Kwan, Hoi Leong Xavier Wong, Yang Chen, Silong Sun, Xuefeng Xie, Xiaodong Fang, Huanming Yang, Jian Wang, Lixin Zhu…

Direct and indirect effects of a pH gradient bring insights into the mechanisms driving prokaryotic community structures

pH is frequently reported as the main driver for prokaryotic community structure in soils. However, pH changes are also linked to “spillover effects” on other chemical parameters (e.g., availability of Al, Fe,...

Authors: Daniel R. Lammel, Gabriel Barth, Otso Ovaskainen, Leonardo M. Cruz, Josileia A. Zanatta, Masahiro Ryo, Emanuel M. de Souza and Fábio O. Pedrosa

A de novo approach to disentangle partner identity and function in holobiont systems

Study of meta-transcriptomic datasets involving non-model organisms represents bioinformatic challenges. The production of chimeric sequences and our inability to distinguish the taxonomic origins of the seque...

Authors: Arnaud Meng, Camille Marchet, Erwan Corre, Pierre Peterlongo, Adriana Alberti, Corinne Da Silva, Patrick Wincker, Eric Pelletier, Ian Probert, Johan Decelle, Stéphane Le Crom, Fabrice Not and Lucie Bittner

Bacterial biogeography of adult airways in atopic asthma

Perturbations to the composition and function of bronchial bacterial communities appear to contribute to the pathophysiology of asthma. Unraveling the nature and mechanisms of these complex associations will r...

Authors: Juliana Durack, Yvonne J. Huang, Snehal Nariya, Laura S. Christian, K. Mark Ansel, Avraham Beigelman, Mario Castro, Anne-Marie Dyer, Elliot Israel, Monica Kraft, Richard J. Martin, David T. Mauger, Sharon R. Rosenberg, Tonya S. King, Steven R. White, Loren C. Denlinger…

Huddling remodels gut microbiota to reduce energy requirements in a small mammal species during cold exposure

Huddling is highly evolved as a cooperative behavioral strategy for social mammals to maximize their fitness in harsh environments. Huddling behavior can change psychological and physiological responses. The c...

Authors: Xue-Ying Zhang, Gansukh Sukhchuluun, Ting-Bei Bo, Qing-Sheng Chi, Jun-Jie Yang, Bin Chen, Lei Zhang and De-Hua Wang

Insights into the ecology, evolution, and metabolism of the widespread Woesearchaeotal lineages

As a recently discovered member of the DPANN superphylum, Woesearchaeota account for a wide diversity of 16S rRNA gene sequences, but their ecology, evolution, and metabolism remain largely unknown.

Authors: Xiaobo Liu, Meng Li, Cindy J. Castelle, Alexander J. Probst, Zhichao Zhou, Jie Pan, Yang Liu, Jillian F. Banfield and Ji-Dong Gu

Meta-analysis of human genome-microbiome association studies: the MiBioGen consortium initiative

In recent years, human microbiota, especially gut microbiota, have emerged as an important yet complex trait influencing human metabolism, immunology, and diseases. Many studies are investigating the forces un...

Authors: Jun Wang, Alexander Kurilshikov, Djawad Radjabzadeh, Williams Turpin, Kenneth Croitoru, Marc Jan Bonder, Matthew A. Jackson, Carolina Medina-Gomez, Fabian Frost, Georg Homuth, Malte Rühlemann, David Hughes, Han-na Kim, Tim D. Spector, Jordana T. Bell, Claire J. Steves…

Oral microbiota in youth with perinatally acquired HIV infection

Microbially mediated oral diseases can signal underlying HIV/AIDS progression in HIV-infected adults. The role of the oral microbiota in HIV-infected youth is not known. The Adolescent Master Protocol of the P...

Authors: Jacqueline R. Starr, Yanmei Huang, Kyu Ha Lee, C. M. Murphy, Anna-Barbara Moscicki, Caroline H. Shiboski, Mark I. Ryder, Tzy-Jyun Yao, Lina L. Faller, Russell B. Van Dyke and Bruce J. Paster

Thermal processing of food reduces gut microbiota diversity of the host and triggers adaptation of the microbiota: evidence from two vertebrates

Adoption of thermal processing of the diet drives human evolution and gut microbiota diversity changes in a dietary habit-dependent manner. However, whether thermal processing of food triggers gut microbial va...

Authors: Zhimin Zhang and Dapeng Li

Early-life skin microbiota in hospitalized preterm and full-term infants

The infant skin microbiota may serve as a reservoir of bacteria that contribute to neonatal infections and stimulate local and systemic immune development. The objectives of our study were to characterize the ...

Authors: Noelle E. Younge, Félix Araújo-Pérez, Debra Brandon and Patrick C. Seed

Gut microbiota in experimental murine model of Graves’ orbitopathy established in different environments may modulate clinical presentation of disease

Variation in induced models of autoimmunity has been attributed to the housing environment and its effect on the gut microbiota. In Graves’ disease (GD), autoantibodies to the thyrotropin receptor (TSHR) cause...

Authors: Giulia Masetti, Sajad Moshkelgosha, Hedda-Luise Köhling, Danila Covelli, Jasvinder Paul Banga, Utta Berchner-Pfannschmidt, Mareike Horstmann, Salvador Diaz-Cano, Gina-Eva Goertz, Sue Plummer, Anja Eckstein, Marian Ludgate, Filippo Biscarini and Julian Roberto Marchesi