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Noelle A Held, Matthew R McIlvin, Dawn M Moran, Michael T Laub, Mak A Saito
Two-component sensory (TCS) systems link microbial physiology to the environment and thus may play key roles in biogeochemical cycles. In this study, we surveyed the TCS systems of 328 diverse marine bacterial species. We identified lifestyle traits such as copiotrophy and diazotrophy that are associated with larger numbers of TCS system genes within the genome. We compared marine bacterial species with 1,152 reference bacterial species from a variety of habitats and found evidence of extra response regulators in marine genomes...
January 2019: MSystems
Morgan N Price, Jayashree Ray, Anthony T Iavarone, Hans K Carlson, Elizabeth M Ryan, Rex R Malmstrom, Adam P Arkin, Adam M Deutschbauer
Using genome-wide mutant fitness assays in diverse bacteria, we identified novel oxidative pathways for the catabolism of 2-deoxy-d-ribose and 2-deoxy-d-ribonate. We propose that deoxyribose is oxidized to deoxyribonate, oxidized to ketodeoxyribonate, and cleaved to acetyl coenzyme A (acetyl-CoA) and glyceryl-CoA. We have genetic evidence for this pathway in three genera of bacteria, and we confirmed the oxidation of deoxyribose to ketodeoxyribonate in vitro . In Pseudomonas simiae, the expression of enzymes in the pathway is induced by deoxyribose or deoxyribonate, while in Paraburkholderia bryophila and in Burkholderia phytofirmans, the pathway proceeds in parallel with the known deoxyribose 5-phosphate aldolase pathway...
January 2019: MSystems
Robin Tecon, Sara Mitri, Davide Ciccarese, Dani Or, Jan Roelof van der Meer, David R Johnson
Microbial communities are inherently complex systems. To address this complexity, microbial ecologists are developing new, more elaborate laboratory models at an ever-increasing pace. These model microbial communities and habitats have opened up the exploration of new territories that lie between the simplicity and controllability of "synthetic" systems and the convolution and complexity of natural environments. Here, we discuss this classic methodological divide, we propose a conceptual perspective that integrates new research developments, and we sketch a 3-point possible roadmap to cross the divide between controllability and complexity in microbial ecology...
January 2019: MSystems
Yan Zhu, Jinxin Zhao, Mohd Hafidz Mahamad Maifiah, Tony Velkov, Falk Schreiber, Jian Li
Multidrug-resistant (MDR) Acinetobacter baumannii has emerged as a very problematic pathogen over the past decades, with a high incidence in nosocomial infections. Discovered in the late 1940s but abandoned in the 1970s, polymyxins (i.e., polymyxin B and colistin) have been revived as the last-line therapy against Gram-negative "superbugs," including MDR A. baumannii. Worryingly, resistance to polymyxins in A. baumannii has been increasingly reported, urging the development of novel antimicrobial therapies to rescue this last-line class of antibiotics...
January 2019: MSystems
Mingbang Wang, Jing Wan, Han Rong, Fusheng He, Hui Wang, Jiaxiu Zhou, Chunquan Cai, Yan Wang, Ruihuan Xu, Zhaoqing Yin, Wenhao Zhou
Changes in the gut microenvironment may influence the pathogenesis of autism spectrum disorders (ASD). Here, we investigated the composition of the gut microbiota and metabolites in children with ASD. Ninety-two children with ASD and 42 age-matched children exhibiting typical development (TD) were enrolled in the two-stage study. In the discovery stage, shotgun metagenomic sequencing and liquid chromatography-mass spectrometry (LC-MS) were performed simultaneously on fecal samples obtained from 43 children in the ASD group and 31 children in the TD group...
January 2019: MSystems
Zhenjiang Zech Xu, Amnon Amir, Jon Sanders, Qiyun Zhu, James T Morton, Molly C Bletz, Anupriya Tripathi, Shi Huang, Daniel McDonald, Lingjing Jiang, Rob Knight
Microbiome analyses can be challenging because microbial strains are numerous, and often, confounding factors in the data set are also numerous. Many tools reduce, summarize, and visualize these high-dimensional data to provide insight at the community level. However, they lose the detailed information about each taxon and can be misleading (for example, the well-known horseshoe effect in ordination plots). Thus, multiple methods at different levels of resolution are required to capture the full range of microbial patterns...
January 2019: MSystems
Barbara U Metzler-Zebeli, Sina-Catherine Siegerstetter, Elizabeth Magowan, Peadar G Lawlor, Renée M Petri, Niamh E O Connell, Qendrim Zebeli
Differences in chickens' feed intake may be the underlying factor influencing feed-efficiency (FE)-associated variation in intestinal microbiota and physiology. In chickens eating the same amount of feed, quantitative feed restriction may create similar intestinal conditions and help clarify this cause-and-effect relationship. This study investigated the effect of ad libitum versus restrictive feeding (85% of ad libitum ) on ileal and cecal microbiota, concentrations of short-chain fatty acids, visceral organ size, intestinal morphology, permeability, and expression of genes related to nutrient uptake, barrier function, and innate immune response in broiler chickens with divergent residual feed intake (RFI; metric for FE)...
January 2019: MSystems
Sigal Leviatan, Eran Segal
Shotgun sequencing of samples taken from the human microbiome often reveals only partial mapping of the sequenced metagenomic reads to existing reference genomes. Such partial mappability indicates that many genomes are missing in our reference genome set. This is particularly true for non-Western populations and for samples that do not originate from the gut. Pasolli et al. (E. Pasolli, F. Asnicar, S. Manara, M. Zolfo, et al., Cell, 2019, perform a grand effort to expand the reference set, and to better classify its members, revealing a wider pangenome of existing species as well as identifying new species of previously unknown taxonomic branches...
January 2019: MSystems
Yangyang Jia, Marcus H Y Leung, Xinzhao Tong, David Wilkins, Patrick K H Lee
Microbial communities are composed of populations with vastly different abundances and levels of metabolic and replicative activity, ranging from actively metabolizing and dividing to dormant or nonviable. The 16S rRNA/rDNA ratio is an emerging tool for evaluating cell-level metabolic activity independent of abundance. In this study, we used five long-term enriched model anaerobic digestion (AD) communities to investigate community composition, diversity, structure, and in particular activity based on the rRNA/rDNA ratio...
January 2019: MSystems
Ryan A Blaustein, Alexander G McFarland, Sarah Ben Maamar, Alberto Lopez, Sarah Castro-Wallace, Erica M Hartmann
Understanding underlying mechanisms involved in microbial persistence in the built environment (BE) is essential for strategically mitigating potential health risks. To test the hypothesis that BEs impose selective pressures resulting in characteristic adaptive responses, we performed a pangenomics meta-analysis leveraging 189 genomes (accessed from GenBank) of two epidemiologically important taxa, Bacillus cereus and Staphylococcus aureus, isolated from various origins: the International Space Station (ISS; a model BE), Earth-based BEs, soil, and humans...
January 2019: MSystems
Mei-Ling Han, Yan Zhu, Darren J Creek, Yu-Wei Lin, Alina D Gutu, Paul Hertzog, Tony Purcell, Hsin-Hui Shen, Samuel M Moskowitz, Tony Velkov, Jian Li
Polymyxins are a last-line therapy against multidrug-resistant Pseudomonas aeruginosa; however, resistance to polymyxins has been increasingly reported. Therefore, understanding the mechanisms of polymyxin activity and resistance is crucial for preserving their clinical usefulness. This study employed comparative metabolomics and transcriptomics to investigate the responses of polymyxin-susceptible P. aeruginosa PAK (polymyxin B MIC, 1 mg/liter) and its polymyxin-resistant pmrB mutant PAK pmrB6 (MIC, 16 mg/liter) to polymyxin B (4, 8, and 128 mg/liter) at 1, 4, and 24 h, respectively...
January 2019: MSystems
Jack A Gilbert
No abstract text is available yet for this article.
November 2018: MSystems
Yaqiang Bai, Jia Tao, Jiaorui Zhou, Qingjie Fan, Man Liu, Yuqi Hu, Yao Xu, Lilong Zhang, Jieli Yuan, Wenzhe Li, Xiaolei Ze, Patrice Malard, Zhimou Guo, Jingyu Yan, Ming Li
The milk glycobiome has a significant impact on the gut microbiota of infants, which plays a pivotal role in health and development. Fucosylated human milk oligosaccharides (HMOs) and N-glycans on milk proteins are beneficial for the development of healthy gut microbiota, and the fucosylation levels of these glycans can be affected by the maternal fucosyltransferase 2 gene ( FUT2 ). Here, we present results of longitudinal research on paired milk and stool samples from 56 Chinese mothers (CMs) and their breast-fed children...
November 2018: MSystems
Kristina Bayer, Martin T Jahn, Beate M Slaby, Lucas Moitinho-Silva, Ute Hentschel
Members of the widespread bacterial phylum Chloroflexi can dominate high-microbial-abundance (HMA) sponge microbiomes. In the Sponge Microbiome Project, Chloroflexi sequences amounted to 20 to 30% of the total microbiome of certain HMA sponge genera with the classes/clades SAR202, Caldilineae , and Anaerolineae being the most prominent. We performed metagenomic and single-cell genomic analyses to elucidate the functional gene repertoire of Chloroflexi symbionts of Aplysina aerophoba. Eighteen draft genomes were reconstructed and placed into phylogenetic context of which six were investigated in detail...
November 2018: MSystems
Irina M Velsko, Brinta Chakraborty, Marcelle M Nascimento, Robert A Burne, Vincent P Richards
Health-associated oral Streptococcus species are promising probiotic candidates to protect against dental caries. Ammonia production through the arginine deiminase system (ADS), which can increase the pH of oral biofilms, and direct antagonism of caries-associated bacterial species are desirable properties for oral probiotic strains. ADS and antagonistic activities can vary dramatically among individuals, but the genetic basis for these differences is unknown. We sequenced whole genomes of a diverse set of clinical oral Streptococcus isolates and examined the genetic basis of variability in ADS and antagonistic activities...
November 2018: MSystems
Brittany A Leigh, Sarah R Bordenstein, Andrew W Brooks, Aram Mikaelyan, Seth R Bordenstein
Phylosymbiosis was recently proposed to describe the eco-evolutionary pattern whereby the ecological relatedness (e.g., beta diversity relationships) of host-associated microbial communities parallels the phylogeny of the host species. Representing the most abundant biological entities on the planet and common members of the animal-associated microbiome, viruses can be influential members of host-associated microbial communities that may recapitulate, reinforce, or ablate phylosymbiosis. Here we sequence the metagenomes of purified viral communities from three different parasitic wasp Nasonia species, one cytonuclear introgression line of Nasonia , and the flour moth outgroup Ephestia kuehniella...
November 2018: MSystems
Ashkaan K Fahimipour, Sarah Ben Mamaar, Alexander G McFarland, Ryan A Blaustein, Jing Chen, Adam J Glawe, Jeff Kline, Jessica L Green, Rolf U Halden, Kevin Van Den Wymelenberg, Curtis Huttenhower, Erica M Hartmann
Humans purposefully and inadvertently introduce antimicrobial chemicals into buildings, resulting in widespread compounds, including triclosan, triclocarban, and parabens, in indoor dust. Meanwhile, drug-resistant infections continue to increase, raising concerns that buildings function as reservoirs of, or even select for, resistant microorganisms. Support for these hypotheses is limited largely since data describing relationships between antimicrobials and indoor microbial communities are scant. We combined liquid chromatography-isotope dilution tandem mass spectrometry with metagenomic shotgun sequencing of dust collected from athletic facilities to characterize relationships between indoor antimicrobial chemicals and microbial communities...
November 2018: MSystems
A S Gargis, H P McLaughlin, A B Conley, C Lascols, P A Michel, J E Gee, C K Marston, C B Kolton, L M Rodriguez-R, A R Hoffmaster, L M Weigel, D Sue
Penicillin (PEN) is a low-cost option for anthrax treatment, but naturally occurring resistance has been reported. β-Lactamase expression ( bla1 , bla2 ) in Bacillus anthracis is regulated by a sigma factor (SigP) and its cognate anti-sigma factor (RsiP). Mutations leading to truncation of RsiP were previously described as a basis for PEN resistance. Here, we analyze whole-genome sequencing (WGS) data and compare the chromosomal sigP-bla1 regions from 374 B. anthracis strains to determine the frequency of mutations, identify mutations associated with PEN resistance, and evaluate the usefulness of WGS for predicting PEN resistance...
November 2018: MSystems
Isabel F Escapa, Tsute Chen, Yanmei Huang, Prasad Gajare, Floyd E Dewhirst, Katherine P Lemon
The expanded Human Oral Microbiome Database (eHOMD) is a comprehensive microbiome database for sites along the human aerodigestive tract that revealed new insights into the nostril microbiome. The eHOMD provides well-curated 16S rRNA gene reference sequences linked to available genomes and enables assignment of species-level taxonomy to most next-generation sequences derived from diverse aerodigestive tract sites, including the nasal passages, sinuses, throat, esophagus, and mouth. Using minimum entropy decomposition coupled with the RDP Classifier and our eHOMD V1-V3 training set, we reanalyzed 16S rRNA V1-V3 sequences from the nostrils of 210 Human Microbiome Project participants at the species level, revealing four key insights...
November 2018: MSystems
Matthew Chung, James B Munro, Hervé Tettelin, Julie C Dunning Hotopp
With the exponential increase in the number of bacterial taxa with genome sequence data, a new standardized method to assign species designations is needed that is consistent with classically obtained taxonomic analyses. This is particularly acute for unculturable, obligate intracellular bacteria with which classically defined methods, like DNA-DNA hybridization, cannot be used, such as those in the Rickettsiales . In this study, we generated nucleotide-based core genome alignments for a wide range of genera with classically defined species, as well as those within the Rickettsiales ...
November 2018: MSystems
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