Articles

Decoding the RNA viromes in rodent lungs provides new insight into the origin and evolutionary patterns of rodent-borne pathogens in Mainland Southeast Asia

As the largest group of mammalian species, which are also widely distributed all over the world, rodents are the natural reservoirs for many diverse zoonotic viruses. A comprehensive understanding of the core ...

Authors: Zhiqiang Wu, Yelin Han, Bo Liu, Hongying Li, Guangjian Zhu, Alice Latinne, Jie Dong, Lilin Sun, Haoxiang Su, Liguo Liu, Jiang Du, Siyu Zhou, Mingxing Chen, Anamika Kritiyakan, Sathaporn Jittapalapong, Kittipong Chaisiri…

Whole microbial community viability is not quantitatively reflected by propidium monoazide sequencing approach

High-throughput sequencing provides a powerful window into the structural and functional profiling of microbial communities, but it is unable to characterize only the viable portion of microbial communities at...

Authors: Ya Wang, Yan Yan, Kelsey N. Thompson, Sena Bae, Emma K. Accorsi, Yancong Zhang, Jiaxian Shen, Hera Vlamakis, Erica M. Hartmann and Curtis Huttenhower

Understanding the host-microbe interactions using metabolic modeling

The human gut harbors an enormous number of symbiotic microbes, which is vital for human health. However, interactions within the complex microbiota community and between the microbiota and its host are challe...

Authors: Jack Jansma and Sahar El Aidy

Bacterial community assemblages in classroom floor dust of 50 public schools in a large city: characterization using 16S rRNA sequences and associations with environmental factors

Characterizing indoor microbial communities using molecular methods provides insight into bacterial assemblages present in environments that can influence occupants’ health. We conducted an environmental asses...

Authors: Ju-Hyeong Park, Angela R. Lemons, Jerry Roseman, Brett J. Green and Jean M. Cox-Ganser

Low-dosage ozonation in gas-phase biofilter promotes community diversity and robustness

The ozonation of biofilters is known to alleviate clogging and pressure drop issues while maintaining removal performances in biofiltration systems treating gaseous volatile organic compounds (VOCs). The effec...

Authors: Marvin Yeung, Prakit Saingam, Yang Xu and Jinying Xi

Polinton-like viruses are abundant in aquatic ecosystems

Polintons are large mobile genetic elements found in the genomes of eukaryotic organisms that are considered the ancient ancestors of most eukaryotic dsDNA viruses. Originally considered as transposons, they h...

Authors: Christopher M. Bellas and Ruben Sommaruga

A semi-tryptic peptide centric metaproteomic mining approach and its potential utility in capturing signatures of gut microbial proteolysis

Proteolysis regulation allows gut microbes to respond rapidly to dynamic intestinal environments by fast degradation of misfolded proteins and activation of regulatory proteins. However, alterations of gut mic...

Authors: Zhixiang Yan, Feixiang He, Fei Xiao, Huanhuan He, Dan Li, Li Cong, Lu Lin, Huijin Zhu, Yanyan Wu, Ru Yan, Xiaofeng Li and Hong Shan

High-dose saccharin supplementation does not induce gut microbiota changes or glucose intolerance in healthy humans and mice

Non-caloric artificial sweeteners (NCAS) are widely used as a substitute for dietary sugars to control body weight or glycemia. Paradoxically, some interventional studies in humans and rodents have shown unfav...

Authors: Joan Serrano, Kathleen R. Smith, Audra L. Crouch, Vandana Sharma, Fanchao Yi, Veronika Vargova, Traci E. LaMoia, Lydia M. Dupont, Vanida Serna, Fenfen Tang, Laisa Gomes-Dias, Joshua J. Blakeslee, Emmanuel Hatzakis, Scott N. Peterson, Matthew Anderson, Richard E. Pratley…

Corroborating evidence refutes batch effect as explanation for fetal bacteria

Authors: E. Rackaityte, J. Halkias, E. M. Fukui, V. F. Mendoza, C. Hayzelden, E. D. Crawford, K. E. Fujimura, T. D. Burt and S. V. Lynch

Microbiome or no microbiome: are we looking at the prenatal environment through the right lens?

Authors: W. Florian Fricke and Jacques Ravel

Lessons learned from the prenatal microbiome controversy

For more than a century, the prenatal environment was considered sterile. Over the last few years, findings obtained with next-generation sequencing approaches from samples of the placenta, the amniotic fluid,...

Authors: Martin J. Blaser, Suzanne Devkota, Kathy D. McCoy, David A. Relman, Moran Yassour and Vincent B. Young

Group therapy on in utero colonization: seeking common truths and a way forward

The human microbiome refers to the genetic composition of microorganisms in a particular location in the human body. Emerging evidence over the past many years suggests that the microbiome constitute drivers o...

Authors: Rachel B. Silverstein and Indira U. Mysorekar

Batch effects account for the main findings of an in utero human intestinal bacterial colonization study

A recent study by Rackaityte et al. reported evidence for a low level of bacterial colonization, specifically of Micrococcus luteus, in the intestine of second trimester human fetuses. We have re-analyzed their s...

Authors: Marcus C. de Goffau, D. Stephen Charnock-Jones, Gordon C. S. Smith and Julian Parkhill

A philosophical perspective on the prenatal in utero microbiome debate

Within the last 6 years, a research field has emerged that focuses on the characterization of microbial communities in the prenatal intrauterine environment of humans and their putative role in human health. H...

Authors: Jens Walter and Mathias W. Hornef

Re-purposing software for functional characterization of the microbiome

Widespread bioinformatic resource development generates a constantly evolving and abundant landscape of workflows and software. For analysis of the microbiome, workflows typically begin with taxonomic classifi...

Authors: Laura-Jayne Gardiner, Niina Haiminen, Filippo Utro, Laxmi Parida, Ed Seabolt, Ritesh Krishna and James H. Kaufman

Comment on “Conserved phylogenetic distribution and limited antibiotic resistance of class 1 integrons revealed by assessing the bacterial genome and plasmid collection” by A.N. Zhang et al.

An article published in Microbiome in July 2018 uses incorrect definitions of integron integrase IntI1 and of class 1 integrons that affect the interpretation of the data.

Authors: Paul H. Roy, Sally R. Partridge and Ruth M. Hall

Microbiome for Mars: surveying microbiome connections to healthcare with implications for long-duration human spaceflight, virtual workshop, July 13, 2020

The inaugural “Microbiome for Mars” virtual workshop took place on July 13, 2020. This event assembled leaders in microbiome research and development to discuss their work and how it may relate to long-duratio...

Authors: Michael LaPelusa, Dorit Donoviel, Sergio E. Branzini, Paul E. Carlson Jr, Stephanie Culler, Amrita K. Cheema, Rima Kaddurah-Daouk, Denise Kelly, Isabelle de Cremoux, Rob Knight, Rosa Krajmalnik-Brown, Stephen L. Mayo, Sarkis K. Mazmanian, Emeran A. Mayer, Joseph F. Petrosino and Keith Garrison

Sensitive universal detection of blood parasites by selective pathogen-DNA enrichment and deep amplicon sequencing

Targeted amplicon deep sequencing (TADS) has enabled characterization of diverse bacterial communities, yet the application of TADS to communities of parasites has been relatively slow to advance. The greatest...

Authors: Briana R. Flaherty, Joel Barratt, Meredith Lane, Eldin Talundzic and Richard S. Bradbury

Roundup causes embryonic development failure and alters metabolic pathways and gut microbiota functionality in non-target species

Research around the weedkiller Roundup is among the most contentious of the twenty-first century. Scientists have provided inconclusive evidence that the weedkiller causes cancer and other life-threatening dis...

Authors: Antonio Suppa, Jouni Kvist, Xiaojing Li, Vignesh Dhandapani, Hanan Almulla, Antoine Y. Tian, Stephen Kissane, Jiarui Zhou, Alessio Perotti, Hayley Mangelson, Kyle Langford, Valeria Rossi, James B. Brown and Luisa Orsini

Correction to: The chemodiversity of paddy soil dissolved organic matter correlates with microbial community at continental scales

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

Authors: Hong-Yi Li, Hang Wang, Hai-Tao Wang, Pei-Yong Xin, Xin-Hua Xu, Yun Ma, Wei-Ping Liu, Chang-Yun Teng, Cheng-Liang Jiang, Li-Ping Lou, Wyatt Arnold, Lauren Cralle, Yong-Guan Zhu, Jin-Fang Chu, Jack A. Gilbert and Zhi-Jian Zhang

Genetic selection for growth drives differences in intestinal microbiota composition and parasite disease resistance in gilthead sea bream

The key effects of intestinal microbiota in animal health have led to an increasing interest in manipulating these bacterial populations to improve animal welfare. The aquaculture sector is no exception and in...

Authors: M. Carla Piazzon, Fernando Naya-Català, Erick Perera, Oswaldo Palenzuela, Ariadna Sitjà-Bobadilla and Jaume Pérez-Sánchez

Perinatal environment shapes microbiota colonization and infant growth: impact on host response and intestinal function

Early microbial colonization triggers processes that result in intestinal maturation and immune priming. Perinatal factors, especially those associated with birth, including both mode and place of delivery are...

Authors: M. Selma-Royo, M. Calatayud Arroyo, I. García-Mantrana, A. Parra-Llorca, R. Escuriet, C. Martínez-Costa and M. C. Collado

VALENCIA: a nearest centroid classification method for vaginal microbial communities based on composition

Taxonomic profiles of vaginal microbial communities can be sorted into a discrete number of categories termed community state types (CSTs). This approach is advantageous because collapsing a hyper-dimensional ...

Authors: Michael T. France, Bing Ma, Pawel Gajer, Sarah Brown, Michael S. Humphrys, Johanna B. Holm, L. Elaine Waetjen, Rebecca M. Brotman and Jacques Ravel

Microbial function and genital inflammation in young South African women at high risk of HIV infection

Female genital tract (FGT) inflammation is an important risk factor for HIV acquisition. The FGT microbiome is closely associated with inflammatory profile; however, the relative importance of microbial activi...

Authors: Arghavan Alisoltani, Monalisa T. Manhanzva, Matthys Potgieter, Christina Balle, Liam Bell, Elizabeth Ross, Arash Iranzadeh, Michelle du Plessis, Nina Radzey, Zac McDonald, Bridget Calder, Imane Allali, Nicola Mulder, Smritee Dabee, Shaun Barnabas, Hoyam Gamieldien…

Antimicrobial use and production system shape the fecal, environmental, and slurry resistomes of pig farms

The global threat of antimicrobial resistance (AMR) is a One Health problem impacted by antimicrobial use (AMU) for human and livestock applications. Extensive Iberian swine production is based on a more susta...

Authors: Oscar Mencía-Ares, Raúl Cabrera-Rubio, José Francisco Cobo-Díaz, Avelino Álvarez-Ordóñez, Manuel Gómez-García, Héctor Puente, Paul D. Cotter, Fiona Crispie, Ana Carvajal, Pedro Rubio and Héctor Argüello

New viral biogeochemical roles revealed through metagenomic analysis of Lake Baikal

Lake Baikal is the largest body of liquid freshwater on Earth. Previous studies have described the microbial composition of this habitat, but the viral communities from this ecosystem have not been characteriz...

Authors: F. H. Coutinho, P. J. Cabello-Yeves, R. Gonzalez-Serrano, R. Rosselli, M. López-Pérez, T. I. Zemskaya, A. S. Zakharenko, V. G. Ivanov and F. Rodriguez-Valera

Characterization of TMAO productivity from carnitine challenge facilitates personalized nutrition and microbiome signatures discovery

The capability of gut microbiota in degrading foods and drugs administered orally can result in diversified efficacies and toxicity interpersonally and cause significant impact on human health. Production of a...

Authors: Wei-Kai Wu, Suraphan Panyod, Po-Yu Liu, Chieh-Chang Chen, Hsien-Li Kao, Hsiao-Li Chuang, Ying-Hsien Chen, Hsin-Bai Zou, Han-Chun Kuo, Ching-Hua Kuo, Ben-Yang Liao, Tina H. T. Chiu, Ching-Hu Chung, Angela Yu-Chen Lin, Yi-Chia Lee, Sen-Lin Tang…

Spatial heterogeneity of bacterial colonization across different gut segments following inter-species microbiota transplantation

The microbiota presents a compartmentalized distribution across different gut segments. Hence, the exogenous microbiota from a particular gut segment might only invade its homologous gut location during microb...

Authors: Na Li, Bin Zuo, Shimeng Huang, Benhua Zeng, Dandan Han, Tiantian Li, Ting Liu, Zhenhua Wu, Hong Wei, Jiangchao Zhao and Junjun Wang

Association of gut microbiota with metabolism in juvenile Atlantic salmon

The gut microbiome plays a key role in animal health and metabolism through the intricate functional interconnection between the feed, gut microbes, and the host. Unfortunately, in aquaculture, the links betwe...

Authors: H. Dvergedal, S. R. Sandve, I. L. Angell, G. Klemetsdal and K. Rudi

Systemic anti-commensal response to fungi analyzed by flow cytometry is related to gut mycobiome ecology

Interest for the study of gut mycobiota in relation with human health and immune homeostasis has increased in the last years. From this perspective, new tools to study the immune/fungal interface are warranted...

Authors: Alicia Moreno-Sabater, Gaelle Autaa, Delphine Sterlin, Amenie Jerbi, Remy Villette, Johanna B. Holm, Christophe Parizot, Sameh Selim, Yaye Senghor, Pascale Ghillani-Dalbin, Claude Bachmeyer, Christophe Hennequin, Guy Gorochov and Martin Larsen

Transductomics: sequencing-based detection and analysis of transduced DNA in pure cultures and microbial communities

Horizontal gene transfer (HGT) plays a central role in microbial evolution. Our understanding of the mechanisms, frequency, and taxonomic range of HGT in polymicrobial environments is limited, as we currently ...

Authors: Manuel Kleiner, Brian Bushnell, Kenneth E. Sanderson, Lora V. Hooper and Breck A. Duerkop

Unravelling the importance of the eukaryotic and bacterial communities and their relationship with Legionella spp. ecology in cooling towers: a complex network

Cooling towers are a major source of large community-associated outbreaks of Legionnaires’ disease, a severe pneumonia. This disease is contracted when inhaling aerosols that are contaminated with bacteria fro...

Authors: Kiran Paranjape, Émilie Bédard, Deeksha Shetty, Mengqi Hu, Fiona Chan Pak Choon, Michèle Prévost and Sébastien P. Faucher

A comprehensive investigation of metagenome assembly by linked-read sequencing

The human microbiota are complex systems with important roles in our physiological activities and diseases. Sequencing the microbial genomes in the microbiota can help in our interpretation of their activities...

Authors: Lu Zhang, Xiaodong Fang, Herui Liao, Zhenmiao Zhang, Xin Zhou, Lijuan Han, Yang Chen, Qinwei Qiu and Shuai Cheng Li

High-quality bacterial genomes of a partial-nitritation/anammox system by an iterative hybrid assembly method

Genome-centric approaches are widely used to investigate microbial compositions, dynamics, ecology, and interactions within various environmental systems. Hundreds or even thousands of genomes could be retriev...

Authors: Lei Liu, Yulin Wang, You Che, Yiqiang Chen, Yu Xia, Ruibang Luo, Suk Hang Cheng, Chunmiao Zheng and Tong Zhang

Shifts in microbial diversity, composition, and functionality in the gut and genital microbiome during a natural SIV infection in vervet monkeys

The microbiota plays an important role in HIV pathogenesis in humans. Microbiota can impact health through several pathways such as increasing inflammation in the gut, metabolites of bacterial origin, and micr...

Authors: Anna J. Jasinska, Tien S. Dong, Venu Lagishetty, William Katzka, Jonathan P. Jacobs, Christopher A. Schmitt, Jennifer Danzy Cramer, Dongzhu Ma, Willem G. Coetzer, J. Paul Grobler, Trudy R. Turner, Nelson Freimer, Ivona Pandrea and Cristian Apetrei

Alternative stable states in the intestinal ecosystem: proof of concept in a rat model and a perspective of therapeutic implications

Chronic immune-mediated diseases are rapidly expanding and notoriously difficult to cure. Altered relatively stable intestinal microbiota configurations are associated with several of these diseases, and with ...

Authors: Maarten Van de Guchte, Sebastian D. Burz, Julie Cadiou, Jiangbo Wu, Stanislas Mondot, Hervé M. Blottière and Joël Doré

Expanding magnetic organelle biogenesis in the domain Bacteria

The discovery of membrane-enclosed, metabolically functional organelles in Bacteria has transformed our understanding of the subcellular complexity of prokaryotic cells. Biomineralization of magnetic nanoparticle...

Authors: Wei Lin, Wensi Zhang, Greig A. Paterson, Qiyun Zhu, Xiang Zhao, Rob Knight, Dennis A. Bazylinski, Andrew P. Roberts and Yongxin Pan

Uncovering the genomic potential of the Amazon River microbiome to degrade rainforest organic matter

The Amazon River is one of the largest in the world and receives huge amounts of terrestrial organic matter (TeOM) from the surrounding rainforest. Despite this TeOM is typically recalcitrant (i.e. resistant t...

Authors: Célio Dias Santos-Júnior, Hugo Sarmento, Fernando Pellon de Miranda, Flávio Henrique-Silva and Ramiro Logares

Molecular repertoire of Deinococcus radiodurans after 1 year of exposure outside the International Space Station within the Tanpopo mission

The extraordinarily resistant bacterium Deinococcus radiodurans withstands harsh environmental conditions present in outer space. Deinococcus radiodurans was exposed for 1 year outside the International Space Sta...

Authors: Emanuel Ott, Yuko Kawaguchi, Denise Kölbl, Elke Rabbow, Petra Rettberg, Maximilian Mora, Christine Moissl-Eichinger, Wolfram Weckwerth, Akihiko Yamagishi and Tetyana Milojevic

Parallel and non-parallel changes of the gut microbiota during trophic diversification in repeated young adaptive radiations of sympatric cichlid fish

Recent increases in understanding the ecological and evolutionary roles of microbial communities have underscored the importance of their hosts’ biology. Yet, little is known about gut microbiota dynamics duri...

Authors: Andreas Härer, Julián Torres-Dowdall, Sina J. Rometsch, Elizabeth Yohannes, Gonzalo Machado-Schiaffino and Axel Meyer

Correction to: Hill-based dissimilarity indices and null models for analysis of microbial community assembly

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

Authors: Oskar Modin, Raquel Liébana, Soroush Saheb-Alam, Britt-Marie Wilén, Carolina Suarez, Malte Hermansson and Frank Persson

Early-life gut dysbiosis linked to juvenile mortality in ostriches

Imbalances in the gut microbial community (dysbiosis) of vertebrates have been associated with several gastrointestinal and autoimmune diseases. However, it is unclear which taxa are associated with gut dysbio...

Authors: Elin Videvall, Se Jin Song, Hanna M. Bensch, Maria Strandh, Anel Engelbrecht, Naomi Serfontein, Olof Hellgren, Adriaan Olivier, Schalk Cloete, Rob Knight and Charlie K. Cornwallis

Ontogeny, species identity, and environment dominate microbiome dynamics in wild populations of kissing bugs (Triatominae)

Kissing bugs (Triatominae) are blood-feeding insects best known as the vectors of Trypanosoma cruzi, the causative agent of Chagas’ disease. Considering the high epidemiological relevance of these vectors, their ...

Authors: Joel J. Brown, Sonia M. Rodríguez-Ruano, Anbu Poosakkannu, Giampiero Batani, Justin O. Schmidt, Walter Roachell, Jan Zima Jr, Václav Hypša and Eva Nováková

The interplay between host genetics and the gut microbiome reveals common and distinct microbiome features for complex human diseases

Interest in the interplay between host genetics and the gut microbiome in complex human diseases is increasing, with prior evidence mainly being derived from animal models. In addition, the shared and distinct...

Authors: Fengzhe Xu, Yuanqing Fu, Ting-yu Sun, Zengliang Jiang, Zelei Miao, Menglei Shuai, Wanglong Gou, Chu-wen Ling, Jian Yang, Jun Wang, Yu-ming Chen and Ju-Sheng Zheng

Viral ecogenomics across the Porifera

Viruses directly affect the most important biological processes in the ocean via their regulation of prokaryotic and eukaryotic populations. Marine sponges form stable symbiotic partnerships with a wide divers...

Authors: Cecília Pascelli, Patrick W. Laffy, Emmanuelle Botté, Marija Kupresanin, Thomas Rattei, Miguel Lurgi, Timothy Ravasi and Nicole S. Webster

β-glucan attenuates cognitive impairment via the gut-brain axis in diet-induced obese mice

“Western” style dietary patterns are characterized by a high proportion of highly processed foods rich in fat and low in fiber. This diet pattern is associated with a myriad of metabolic dysfunctions, includin...

Authors: Hongli Shi, Yinghua Yu, Danhong Lin, Peng Zheng, Peng Zhang, Minmin Hu, Qiao Wang, Wei Pan, Xiaoying Yang, Tao Hu, Qianqian Li, Renxian Tang, Feng Zhou, Kuiyang Zheng and Xu-Feng Huang

Trophic interactions as determinants of the arbuscular mycorrhizal fungal community with cascading plant-promoting consequences

The soil mycobiome is composed of a complex and diverse fungal community, which includes functionally diverse species ranging from plant pathogens to mutualists. Among the latter are arbuscular mycorrhizal fun...

Authors: Yuji Jiang, Lu Luan, Kaijie Hu, Manqiang Liu, Ziyun Chen, Stefan Geisen, Xiaoyun Chen, Huixin Li, Qinsong Xu, Michael Bonkowski and Bo Sun

Investigating host-microbiome interactions by droplet based microfluidics

Despite the importance of the mucosal interface between microbiota and the host in gut homeostasis, little is known about the mechanisms of bacterial gut colonization, involving foraging for glycans produced b...

Authors: Alexandra S. Tauzin, Mariana Rangel Pereira, Liisa D. Van Vliet, Pierre-Yves Colin, Elisabeth Laville, Jeremy Esque, Sandrine Laguerre, Bernard Henrissat, Nicolas Terrapon, Vincent Lombard, Marion Leclerc, Joël Doré, Florian Hollfelder and Gabrielle Potocki-Veronese

Faecal microbiota transplant from aged donor mice affects spatial learning and memory via modulating hippocampal synaptic plasticity- and neurotransmission-related proteins in young recipients

The gut-brain axis and the intestinal microbiota are emerging as key players in health and disease. Shifts in intestinal microbiota composition affect a variety of systems; however, evidence of their direct im...

Authors: Alfonsina D’Amato, Lorenzo Di Cesare Mannelli, Elena Lucarini, Angela L. Man, Gwenaelle Le Gall, Jacopo J. V. Branca, Carla Ghelardini, Amedeo Amedei, Eugenio Bertelli, Mari Regoli, Alessandra Pacini, Giulia Luciani, Pasquale Gallina, Annalisa Altera, Arjan Narbad, Massimo Gulisano…

Soil origin and plant genotype structure distinct microbiome compartments in the model legume Medicago truncatula

Understanding the genetic and environmental factors that structure plant microbiomes is necessary for leveraging these interactions to address critical needs in agriculture, conservation, and sustainability. L...

Authors: Shawn P. Brown, Michael A. Grillo, Justin C. Podowski and Katy D. Heath