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Tonya L Ward, Maria Gloria Dominguez-Bello, Tim Heisel, Gabriel Al-Ghalith, Dan Knights, Cheryl A Gale
With the advent of next-generation sequencing and microbial community characterization, we are beginning to understand the key factors that shape early-life microbial colonization and associated health outcomes. Studies characterizing infant microbial colonization have focused mostly on bacteria in the microbiome and have largely neglected fungi (the mycobiome), despite their relevance to mucosal infections in healthy infants. In this pilot study, we characterized the skin, oral, and anal mycobiomes of infants over the first month of life ( n = 17) and the anal and vaginal mycobiomes of mothers ( n = 16) by internal transcribed spacer 2 (ITS2) amplicon sequencing...
May 2018: MSystems
Keaton Stagaman, Tara J Cepon-Robins, Melissa A Liebert, Theresa E Gildner, Samuel S Urlacher, Felicia C Madimenos, Karen Guillemin, J Josh Snodgrass, Lawrence S Sugiyama, Brendan J M Bohannan
Economic development is marked by dramatic increases in the incidence of microbiome-associated diseases, such as autoimmune diseases and metabolic syndromes, but the lifestyle changes that drive alterations in the human microbiome are not known. We measured market integration as a proxy for economically related lifestyle attributes, such as ownership of specific market goods that index degree of market integration and components of traditional and nontraditional (more modern) house structure and infrastructure, and profiled the fecal microbiomes of 213 participants from a contiguous, indigenous Ecuadorian population...
January 2018: MSystems
Amanda J Brinkworth, Mark R Wildung, Rey A Carabeo
Iron is essential for growth and development of Chlamydia . Its long-term starvation in cultured mammalian cells leads to production of aberrant noninfectious chlamydial forms, also known as persistence. Immediate transcriptional responses to iron limitation have not been characterized, leaving a knowledge gap of how Chlamydia regulates its response to changes in iron availability. We used the fast-chelating agent 2,2'-bipyridyl (BPDL) to homogeneously starve Chlamydia trachomatis serovar L2 of iron, starting at 6 or 12 h postinfection...
January 2018: MSystems
Kaneyoshi Yamamoto, Yuki Yamanaka, Tomohiro Shimada, Paramita Sarkar, Myu Yoshida, Neerupma Bhardwaj, Hiroki Watanabe, Yuki Taira, Dipankar Chatterji, Akira Ishihama
The RNA polymerase (RNAP) of Escherichia coli K-12 is a complex enzyme consisting of the core enzyme with the subunit structure α2 ββ'ω and one of the σ subunits with promoter recognition properties. The smallest subunit, omega (the rpoZ gene product), participates in subunit assembly by supporting the folding of the largest subunit, β', but its functional role remains unsolved except for its involvement in ppGpp binding and stringent response. As an initial approach for elucidation of its functional role, we performed in this study ChIP-chip (chromatin immunoprecipitation with microarray technology) analysis of wild-type and rpoZ -defective mutant strains...
January 2018: MSystems
Manish Goswami, Akkipeddi Venkat Satya Surya Narayana Rao
We have previously reported that supplementation of exogenous glutathione (GSH) promotes ciprofloxacin resistance in Escherichia coli by neutralizing antibiotic-induced oxidative stress and by enhancing the efflux of antibiotic. In the present study, we used a whole-genome microarray as a tool to analyze the system-level transcriptomic changes of E. coli on exposure to GSH and/or ciprofloxacin. The microarray data revealed that GSH supplementation affects redox function, transport, acid shock, and virulence genes of E...
January 2018: MSystems
Sylvie Janssens, Michael Schotsaert, Rahul Karnik, Vinod Balasubramaniam, Marion Dejosez, Alexander Meissner, Adolfo García-Sastre, Thomas P Zwaka
Zika virus (ZIKV) infection during early pregnancy can cause microcephaly and associated defects at birth, but whether it can induce neurologic sequelae that appear later in life remains unclear. Using a model of the developing brain based on embryonic stem cell-derived brain organoids, we studied the impact of ZIKV infection on the DNA methylation pattern across the entire genome in selected neural cell types. The virus unexpectedly alters the DNA methylome of neural progenitors, astrocytes, and differentiated neurons at genes that have been implicated in the pathogenesis of a number of brain disorders, most prominently mental retardation and schizophrenia...
January 2018: MSystems
James T Morton, Liam Toran, Anna Edlund, Jessica L Metcalf, Christian Lauber, Rob Knight
[This corrects the article DOI: 10.1128/mSystems.00166-16.].
January 2018: MSystems
Eric R Hester, Sarah F Harpenslager, Josepha M H van Diggelen, Leon L Lamers, Mike S M Jetten, Claudia Lüke, Sebastian Lücker, Cornelia U Welte
Wetland ecosystems are important reservoirs of biodiversity and significantly contribute to emissions of the greenhouse gases CO2, N2O, and CH4. High anthropogenic nitrogen (N) inputs from agriculture and fossil fuel combustion have been recognized as a severe threat to biodiversity and ecosystem functioning, such as control of greenhouse gas emissions. Therefore, it is important to understand how increased N input into pristine wetlands affects the composition and activity of microorganisms, especially in interaction with dominant wetland plants...
January 2018: MSystems
A S Bertuzzi, A M Walsh, J J Sheehan, P D Cotter, F Crispie, P L H McSweeney, K N Kilcawley, M C Rea
In this study, a young Cheddar curd was used to produce two types of surface-ripened cheese, using two commercial smear-culture mixes of yeasts and bacteria. Whole-metagenome shotgun sequencing was used to screen the microbial population within the smear-culture mixes and on the cheese surface, with comparisons of microorganisms at both the species and the strain level. The use of two smear mixes resulted in the development of distinct microbiotas on the surfaces of the two test cheeses. In one case, most of the species inoculated on the cheese established themselves successfully on the surface during ripening, while in the other, some of the species inoculated were not detected during ripening and the most dominant bacterial species, Glutamicibacter arilaitensis, was not a constituent of the culture mix...
January 2018: MSystems
Youlian Zhou, Zhenjiang Zech Xu, Yan He, Yunsheng Yang, Le Liu, Qianyun Lin, Yuqiang Nie, Mingsong Li, Fachao Zhi, Side Liu, Amnon Amir, Antonio González, Anupriya Tripathi, Minhu Chen, Gary D Wu, Rob Knight, Hongwei Zhou, Ye Chen
Gut microbiota dysbiosis contributes to the onset and perpetuation of inflammatory bowel disease (IBD). Given that gut microbiotas vary across geography and ethnicity, it remains obscure whether any universal microbial signatures for IBD diagnosis and prognosis evaluation exist irrespective of populations. Here we profiled the fecal microbiota of a series of Chinese IBD patients and combined them with two Western IBD cohorts, PRISM and RISK, for meta-analyses. We found that the gut microbial alteration patterns in IBD are similar among Chinese and Westerners...
January 2018: MSystems
Tatum D Mortimer, Alexandra M Weber, Caitlin S Pepperell
Tuberculosis (TB) is the leading cause of death by an infectious disease, and global TB control efforts are increasingly threatened by drug resistance in Mycobacterium tuberculosis . Unlike most bacteria, where lateral gene transfer is an important mechanism of resistance acquisition, resistant M. tuberculosis arises solely by de novo chromosomal mutation. Using whole-genome sequencing data from two natural populations of M. tuberculosis , we characterized the population genetics of known drug resistance loci using measures of diversity, population differentiation, and convergent evolution...
January 2018: MSystems
Chandru Subramani, Vidya P Nair, Saumya Anang, Sukhen Das Mandal, Madhu Pareek, Nidhi Kaushik, Akriti Srivastava, Sudipto Saha, Shalimar, Baibaswata Nayak, C T Ranjith-Kumar, Milan Surjit
Comprehensive knowledge of host-pathogen interactions is central to understand the life cycle of a pathogen and devise specific therapeutic strategies. Protein-protein interactions (PPIs) are key mediators of host-pathogen interactions. Hepatitis E virus (HEV) is a major cause of viral hepatitis in humans. Recent reports also demonstrate its extrahepatic manifestations in the brain. Toward understanding the molecular details of HEV life cycle, we screened human liver and fetal brain cDNA libraries to identify the host interaction partners of proteins encoded by genotype 1 HEV and constructed the virus-host PPI network...
January 2018: MSystems
Collin M Timm, Kelsey R Carter, Alyssa A Carrell, Se-Ran Jun, Sara S Jawdy, Jessica M Vélez, Lee E Gunter, Zamin Yang, Intawat Nookaew, Nancy L Engle, Tse-Yuan S Lu, Christopher W Schadt, Timothy J Tschaplinski, Mitchel J Doktycz, Gerald A Tuskan, Dale A Pelletier, David J Weston
Adverse growth conditions can lead to decreased plant growth, productivity, and survival, resulting in poor yields or failure of crops and biofeedstocks. In some cases, the microbial community associated with plants has been shown to alleviate plant stress and increase plant growth under suboptimal growing conditions. A systematic understanding of how the microbial community changes under these conditions is required to understand the contribution of the microbiome to water utilization, nutrient uptake, and ultimately yield...
January 2018: MSystems
Michael Shaffer, Catherine Lozupone
Modern hygienic practices are applied to avoid exposure to pathogens that spread via fecal-oral transmission. Despite this, the gastrointestinal tract is quickly colonized by fecal microbes. The hands are an important vector for the transmission of microbes, but the frequency at which fecal and oral microbes exist on hands and the source of those microbes have not been extensively described. Using data from a previous study that characterized the fecal, oral, and skin microbiota from 73 families, we found a significant incidence of fecal and oral microbes on hands...
January 2018: MSystems
Hualan Liu, Morgan N Price, Robert Jordan Waters, Jayashree Ray, Hans K Carlson, Jacob S Lamson, Romy Chakraborty, Adam P Arkin, Adam M Deutschbauer
Transposon mutagenesis coupled to next-generation sequencing (TnSeq) is a powerful approach for discovering the functions of bacterial genes. However, the development of a suitable TnSeq strategy for a given bacterium can be costly and time-consuming. To meet this challenge, we describe a part-based strategy for constructing libraries of hundreds of transposon delivery vectors, which we term "magic pools." Within a magic pool, each transposon vector has a different combination of upstream sequences (promoters and ribosome binding sites) and antibiotic resistance markers as well as a random DNA barcode sequence, which allows the tracking of each vector during mutagenesis experiments...
January 2018: MSystems
Sumayah F Rahman, Matthew R Olm, Michael J Morowitz, Jillian F Banfield
Antibiotic resistance in pathogens is extensively studied, and yet little is known about how antibiotic resistance genes of typical gut bacteria influence microbiome dynamics. Here, we leveraged genomes from metagenomes to investigate how genes of the premature infant gut resistome correspond to the ability of bacteria to survive under certain environmental and clinical conditions. We found that formula feeding impacts the resistome. Random forest models corroborated by statistical tests revealed that the gut resistome of formula-fed infants is enriched in class D beta-lactamase genes...
January 2018: MSystems
Tom Berben, Cherel Balkema, Dimitry Y Sorokin, Gerard Muyzer
Thiocyanate (N=C-S-) is a moderately toxic, inorganic sulfur compound. It occurs naturally as a by-product of the degradation of glucosinolate-containing plants and is produced industrially in a number of mining processes. Currently, two pathways for the primary degradation of thiocyanate in bacteria are recognized, the carbonyl sulfide pathway and the cyanate pathway, of which only the former has been fully characterized. Use of the cyanate pathway has been shown in only 10 strains of Thioalkalivibrio, a genus of obligately haloalkaliphilic sulfur-oxidizing Gammaproteobacteria found in soda lakes...
November 2017: MSystems
Benoit Delahaye, Damien Eveillard, Nicholas Bouskill
For decades, microbiologists have considered uncertainties as an undesired side effect of experimental protocols. As a consequence, standard microbial system modeling strives to hide uncertainties for the sake of deterministic understanding. However, recent studies have highlighted greater experimental variability than expected and emphasized uncertainties not as a weakness but as a necessary feature of complex microbial systems. We therefore advocate that biological uncertainties need to be considered foundational facets that must be incorporated in models...
November 2017: MSystems
Marius Vital, André Karch, Dietmar H Pieper
Given the key role of butyrate for host health, understanding the ecology of intestinal butyrate-producing communities is a top priority for gut microbiota research. To this end, we performed a pooled analysis on 2,387 metagenomic/transcriptomic samples from 15 publicly available data sets that originated from three continents and encompassed eight diseases as well as specific interventions. For analyses, a gene catalogue was constructed from gene-targeted assemblies of all genes from butyrate synthesis pathways of all samples and from an updated reference database derived from genome screenings...
November 2017: MSystems
Isabelle Laforest-Lapointe, Christian Messier, Steven W Kembel
Tree leaf-associated microbiota have been studied in natural ecosystems but less so in urban settings, where anthropogenic pressures on trees could impact microbial communities and modify their interaction with their hosts. Additionally, trees act as vectors spreading bacterial cells in the air in urban environments due to the density of microbial cells on aerial plant surfaces. Characterizing tree leaf bacterial communities along an urban gradient is thus key to understand the impact of anthropogenic pressures on urban tree-bacterium interactions and on the overall urban microbiome...
November 2017: MSystems
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