Articles

Dynamics of microbial populations mediating biogeochemical cycling in a freshwater lake

Microbial processes are intricately linked to the depletion of oxygen in in-land and coastal water bodies, with devastating economic and ecological consequences. Microorganisms deplete oxygen during biomass de...

Authors: Keith Arora-Williams, Scott W. Olesen, Benjamin P. Scandella, Kyle Delwiche, Sarah J. Spencer, Elise M. Myers, Sonali Abraham, Alyssa Sooklal and Sarah P. Preheim

Restriction enzyme digestion of host DNA enhances universal detection of parasitic pathogens in blood via targeted amplicon deep sequencing

Targeted amplicon deep sequencing (TADS) of the 16S rRNA gene is commonly used to explore and characterize bacterial microbiomes. Meanwhile, attempts to apply TADS to the detection and characterization of enti...

Authors: Briana R. Flaherty, Eldin Talundzic, Joel Barratt, Kristine J. Kines, Christian Olsen, Meredith Lane, Mili Sheth and Richard S. Bradbury

Prokaryotic horizontal gene transfer within the human holobiont: ecological-evolutionary inferences, implications and possibilities

The ubiquity of horizontal gene transfer in the living world, especially among prokaryotes, raises interesting and important scientific questions regarding its effects on the human holobiont i.e., the human an...

Authors: Ramakrishnan Sitaraman

Lignocellulose degradation at the holobiont level: teamwork in a keystone soil invertebrate

Woodlice are recognized as keystone species in terrestrial ecosystems due to their role in the decomposition of organic matter. Thus, they contribute to lignocellulose degradation and nutrient cycling in the e...

Authors: Marius Bredon, Jessica Dittmer, Cyril Noël, Bouziane Moumen and Didier Bouchon

Single-cell genomics of co-sorted Nanoarchaeota suggests novel putative host associations and diversification of proteins involved in symbiosis

Nanoarchaeota are obligate symbionts of other Archaea first discovered 16 years ago, yet little is known about this largely uncultivated taxon. While Nanoarchaeota diversity has been detected in a variety of habi...

Authors: Jessica K. Jarett, Stephen Nayfach, Mircea Podar, William Inskeep, Natalia N. Ivanova, Jacob Munson-McGee, Frederik Schulz, Mark Young, Zackary J. Jay, Jacob P. Beam, Nikos C. Kyrpides, Rex R. Malmstrom, Ramunas Stepanauskas and Tanja Woyke

Translating research to policy at the NCSE 2017 symposium “Microbiology of the Built Environment: Implications for Health and Design”

Here, we summarize a symposium entitled “Microbiology of the Built Environment: Implications for Health and Design” that was presented at the National Council for Science and the Environment (NCSE) 17th Nation...

Authors: Ashleigh Bope, Mark H. Weir, Amy Pruden, Michael Morowitz, Jade Mitchell and Karen C. Dannemiller

Longitudinal development of the dust microbiome in a newly opened Norwegian kindergarten

In Norway, 91% of children aged 1–5 attend kindergarten where they are exposed to indoor microbiomes which can have relevance for development and health. In order to gain a better understanding of the composit...

Authors: Anders B. Nygaard and Colin Charnock

MetaWRAP—a flexible pipeline for genome-resolved metagenomic data analysis

The study of microbiomes using whole-metagenome shotgun sequencing enables the analysis of uncultivated microbial populations that may have important roles in their environments. Extracting individual draft ge...

Authors: Gherman V. Uritskiy, Jocelyne DiRuggiero and James Taylor

Dichotomous development of the gut microbiome in preterm infants

Preterm infants are at risk of developing intestinal dysbiosis with an increased proportion of Gammaproteobacteria. In this study, we sought the clinical determinants of the relative abundance of feces-associa...

Authors: Thao T. B. Ho, Maureen W. Groer, Bradley Kane, Alyson L. Yee, Benjamin A. Torres, Jack A. Gilbert and Akhil Maheshwari

Root exudates drive the soil-borne legacy of aboveground pathogen infection

Plants are capable of building up beneficial rhizosphere communities as is evidenced by disease-suppressive soils. However, it is not known how and why soil bacterial communities are impacted by plant exposure...

Authors: Jun Yuan, Jun Zhao, Tao Wen, Mengli Zhao, Rong Li, Pim Goossens, Qiwei Huang, Yang Bai, Jorge M. Vivanco, George A. Kowalchuk, Roeland L. Berendsen and Qirong Shen

Quantification of variation and the impact of biomass in targeted 16S rRNA gene sequencing studies

Recent advances in sequencing technologies and bioinformatics tools have allowed for large-scale microbiome studies that are rapidly advancing medical research. However, small changes in technique or analysis ...

Authors: Jeffrey M. Bender, Fan Li, Helty Adisetiyo, David Lee, Sara Zabih, Long Hung, Thomas A. Wilkinson, Pia S. Pannaraj, Rosemary C. She, Jennifer Dien Bard, Nicole H. Tobin and Grace M. Aldrovandi

Alteration of the cutaneous microbiome in psoriasis and potential role in Th17 polarization

Psoriasis impacts 1–3% of the world’s population and is characterized by hyper-proliferation of keratinocytes and increased inflammation. At the molecular level, psoriasis is commonly driven by a Th17 response...

Authors: Hsin-Wen Chang, Di Yan, Rasnik Singh, Jared Liu, Xueyan Lu, Derya Ucmak, Kristina Lee, Ladan Afifi, Douglas Fadrosh, John Leech, Kimberly S. Vasquez, Margaret M. Lowe, Michael D. Rosenblum, Tiffany C. Scharschmidt, Susan V. Lynch and Wilson Liao

High-resolution ISR amplicon sequencing reveals personalized oral microbiome

Sequencing of the 16S rRNA gene has been the standard for studying the composition of microbial communities. While it allows identification of bacteria at the level of species, this method does not usually pro...

Authors: Chiranjit Mukherjee, Clifford J. Beall, Ann L. Griffen and Eugene J. Leys

Enterobacteriaceae are essential for the modulation of colitis severity by fungi

Host-microbe balance maintains intestinal homeostasis and strongly influences inflammatory conditions such as inflammatory bowel diseases (IBD). Here we focused on bacteria-fungi interactions and their implica...

Authors: Bruno Sovran, Julien Planchais, Sarah Jegou, Marjolene Straube, Bruno Lamas, Jane Mea Natividad, Allison Agus, Louise Dupraz, Jérémy Glodt, Grégory Da Costa, Marie-Laure Michel, Philippe Langella, Mathias L. Richard and Harry Sokol

Detecting eukaryotic microbiota with single-cell sensitivity in human tissue

Fetal growth restriction, pre-eclampsia, and pre-term birth are major adverse pregnancy outcomes. These complications are considerable contributors to fetal/maternal morbidity and mortality worldwide. A signif...

Authors: Susanne Lager, Marcus C. de Goffau, Ulla Sovio, Sharon J. Peacock, Julian Parkhill, D. Stephen Charnock-Jones and Gordon C. S. Smith

Influence of cigarette smoking on the human duodenal mucosa-associated microbiota

Cigarette smoking is a known risk factor in a number of gastrointestinal (GI) diseases in which the microbiota is implicated, including duodenal ulcer and Crohn’s disease. Smoking has the potential to alter th...

Authors: Erin R. Shanahan, Ayesha Shah, Natasha Koloski, Marjorie M. Walker, Nicholas J. Talley, Mark Morrison and Gerald J. Holtmann

A multi-source domain annotation pipeline for quantitative metagenomic and metatranscriptomic functional profiling

Biochemical and regulatory pathways have until recently been thought and modelled within one cell type, one organism and one species. This vision is being dramatically changed by the advent of whole microbiome...

Authors: Ari Ugarte, Riccardo Vicedomini, Juliana Bernardes and Alessandra Carbone

Factors shaping the gut bacterial community assembly in two main Colombian malaria vectors

The understanding of the roles of gut bacteria in the fitness and vectorial capacity of mosquitoes that transmit malaria, is improving; however, the factors shaping the composition and structure of such bacter...

Authors: Priscila Bascuñán, Juan Pablo Niño-Garcia, Yadira Galeano-Castañeda, David Serre and Margarita M. Correa

Skin microbiome of coral reef fish is highly variable and driven by host phylogeny and diet

The surface of marine animals is covered by abundant and diversified microbial communities, which have major roles for the health of their host. While such microbiomes have been deeply examined in marine inverteb...

Authors: Marlène Chiarello, Jean-Christophe Auguet, Yvan Bettarel, Corinne Bouvier, Thomas Claverie, Nicholas A. J. Graham, Fabien Rieuvilleneuve, Elliot Sucré, Thierry Bouvier and Sébastien Villéger

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