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Microbiome

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https://www.readbyqxmd.com/read/28724443/metagenomics-of-urban-sewage-identifies-an-extensively-shared-antibiotic-resistome-in-china
#1
Jian-Qiang Su, Xin-Li An, Bing Li, Qing-Lin Chen, Michael R Gillings, Hong Chen, Tong Zhang, Yong-Guan Zhu
BACKGROUND: Antibiotic-resistant pathogens are challenging treatment of infections worldwide. Urban sewage is potentially a major conduit for dissemination of antibiotic resistance genes into various environmental compartments. However, the diversity and abundance of such genes in wastewater are not well known. METHODS: Here, seasonal and geographical distributions of antibiotic resistance genes and their host bacterial communities from Chinese urban sewage were characterized, using metagenomic analyses and 16S rRNA gene-based Illumina sequencing, respectively...
July 19, 2017: Microbiome
https://www.readbyqxmd.com/read/28724405/environmental-drivers-of-viral-community-composition-in-antarctic-soils-identified-by-viromics
#2
Evelien M Adriaenssens, Rolf Kramer, Marc W Van Goethem, Thulani P Makhalanyane, Ian Hogg, Don A Cowan
BACKGROUND: The Antarctic continent is considered the coldest and driest place on earth with simple ecosystems, devoid of higher plants. Soils in the ice-free regions of Antarctica are known to harbor a wide range of microorganisms from primary producers to grazers, yet their ecology and particularly the role of viruses is poorly understood. In this study, we examined the virus community structures of 14 soil samples from the Mackay Glacier region. METHODS: Viral communities were extracted from soil and the dsDNA was extracted, amplified using single-primer amplification, and sequenced using the Ion Torrent Proton platform...
July 19, 2017: Microbiome
https://www.readbyqxmd.com/read/28724401/deciphering-functional-diversification-within-the-lichen-microbiota-by-meta-omics
#3
Tomislav Cernava, Armin Erlacher, Ines Aline Aschenbrenner, Lisa Krug, Christian Lassek, Katharina Riedel, Martin Grube, Gabriele Berg
BACKGROUND: Recent evidence of specific bacterial communities extended the traditional concept of fungal-algal lichen symbioses by a further organismal kingdom. Although functional roles were already assigned to dominant members of the highly diversified microbiota, a substantial fraction of the ubiquitous colonizers remained unexplored. We employed a multi-omics approach to further characterize functional guilds in an unconventional model system. RESULTS: The general community structure of the lichen-associated microbiota was shown to be highly similar irrespective of the employed omics approach...
July 19, 2017: Microbiome
https://www.readbyqxmd.com/read/28716113/whole-metagenome-profiles-of-particulates-collected-from-the-international-space-station
#4
Nicholas A Be, Aram Avila-Herrera, Jonathan E Allen, Nitin Singh, Aleksandra Checinska Sielaff, Crystal Jaing, Kasthuri Venkateswaran
BACKGROUND: The built environment of the International Space Station (ISS) is a highly specialized space in terms of both physical characteristics and habitation requirements. It is unique with respect to conditions of microgravity, exposure to space radiation, and increased carbon dioxide concentrations. Additionally, astronauts inhabit a large proportion of this environment. The microbial composition of ISS particulates has been reported; however, its functional genomics, which are pertinent due to potential impact of its constituents on human health and operational mission success, are not yet characterized...
July 17, 2017: Microbiome
https://www.readbyqxmd.com/read/28709472/potential-and-active-functions-in-the-gut-microbiota-of-a-healthy-human-cohort
#5
Alessandro Tanca, Marcello Abbondio, Antonio Palomba, Cristina Fraumene, Valeria Manghina, Francesco Cucca, Edoardo Fiorillo, Sergio Uzzau
BACKGROUND: The study of the gut microbiota (GM) is rapidly moving towards its functional characterization by means of shotgun meta-omics. In this context, there is still no consensus on which microbial functions are consistently and constitutively expressed in the human gut in physiological conditions. Here, we selected a cohort of 15 healthy subjects from a native and highly monitored Sardinian population and analyzed their GMs using shotgun metaproteomics, with the aim of investigating GM functions actually expressed in a healthy human population...
July 14, 2017: Microbiome
https://www.readbyqxmd.com/read/28709450/-dis-trust-your-gut-the-gut-microbiome-in-age-related-inflammation-health-and-disease
#6
REVIEW
Thomas W Buford
Chronic inflammation represents one of the most consistent biologic features of aging. However, the precise etiology of persistent low-grade increases in inflammation remains unclear. Recent evidence suggests that the gut microbiome may play a key role in age-related inflammation. Indeed, several studies have indicated that older adults display an altered composition of the gut microbiota, and early evidence indicates that this dysbiosis is associated with the presence of several key circulating inflammatory analytes...
July 14, 2017: Microbiome
https://www.readbyqxmd.com/read/28705228/cleanliness-in-context-reconciling-hygiene-with-a-modern-microbial-perspective
#7
REVIEW
Roo Vandegrift, Ashley C Bateman, Kyla N Siemens, May Nguyen, Hannah E Wilson, Jessica L Green, Kevin G Van Den Wymelenberg, Roxana J Hickey
The concept of hygiene is rooted in the relationship between cleanliness and the maintenance of good health. Since the widespread acceptance of the germ theory of disease, hygiene has become increasingly conflated with sterilization. In reviewing studies across the hygiene literature (most often hand hygiene), we found that nearly all studies of hand hygiene utilize bulk reduction in bacterial load as a proxy for reduced transmission of pathogenic organisms. This treatment of hygiene may be insufficient in light of recent microbial ecology research, which has demonstrated that humans have intimate and evolutionarily significant relationships with a diverse assemblage of microorganisms (our microbiota)...
July 14, 2017: Microbiome
https://www.readbyqxmd.com/read/28705224/more-than-just-a-gut-feeling-constraint-based-genome-scale-metabolic-models-for-predicting-functions-of-human-intestinal-microbes
#8
REVIEW
Kees C H van der Ark, Ruben G A van Heck, Vitor A P Martins Dos Santos, Clara Belzer, Willem M de Vos
The human gut is colonized with a myriad of microbes, with substantial interpersonal variation. This complex ecosystem is an integral part of the gastrointestinal tract and plays a major role in the maintenance of homeostasis. Its dysfunction has been correlated to a wide array of diseases, but the understanding of causal mechanisms is hampered by the limited amount of cultured microbes, poor understanding of phenotypes, and the limited knowledge about interspecies interactions. Genome-scale metabolic models (GEMs) have been used in many different fields, ranging from metabolic engineering to the prediction of interspecies interactions...
July 14, 2017: Microbiome
https://www.readbyqxmd.com/read/28705171/formula-diet-driven-microbiota-shifts-tryptophan-metabolism-from-serotonin-to-tryptamine-in-neonatal-porcine-colon%C3%AF
#9
Manish Kumar Saraf, Brian D Piccolo, Anne K Bowlin, Kelly E Mercer, Tanya LeRoith, Sree V Chintapalli, Kartik Shankar, Thomas M Badger, Laxmi Yeruva
BACKGROUND: The gut microbiota of breast-fed and formula-fed infants differ significantly, as do the risks for allergies, gut dysfunction, and upper respiratory tract infections. The connections between breast milk, various formulas, and the profiles of gut bacteria to these childhood illnesses, as well as the mechanisms underlying the effects, are not well understood. METHODS: We investigated distal colon microbiota by 16S RNA amplicon sequencing, morphology by histomorphometry, immune response by cytokine expression, and tryptophan metabolism in a pig model in which piglets were sow-fed, or fed soy or dairy milk-based formula from postnatal day (PND) 2 to 21...
July 14, 2017: Microbiome
https://www.readbyqxmd.com/read/28701177/longitudinal-development-of-the-gut-microbiome-and-metabolome-in-preterm-neonates-with-late-onset-sepsis-and-healthy-controls
#10
Christopher J Stewart, Nicholas D Embleton, Emma C L Marrs, Daniel P Smith, Tatiana Fofanova, Andrew Nelson, Tom Skeath, John D Perry, Joseph F Petrosino, Janet E Berrington, Stephen P Cummings
BACKGROUND: Late onset sepsis (LOS) in preterm infants is associated with considerable morbidity and mortality. While studies have implicated gut bacteria in the aetiology of the disease, functional analysis and mechanistic insights are generally lacking. We performed temporal bacterial (n = 613) and metabolomic (n = 63) profiling on extensively sampled stool from 7 infants with LOS and 28 matched healthy (no LOS or NEC) controls. RESULTS: The bacteria isolated in diagnostic blood culture usually corresponded to the dominant bacterial genera in the gut microbiome...
July 12, 2017: Microbiome
https://www.readbyqxmd.com/read/28701174/normal-milk-microbiome-is-reestablished-following-experimental-infection-with-escherichia-coli-independent-of-intramammary-antibiotic-treatment-with-a-third-generation-cephalosporin-in-bovines
#11
Erika K Ganda, Natalia Gaeta, Anja Sipka, Brianna Pomeroy, Georgios Oikonomou, Ynte H Schukken, Rodrigo C Bicalho
BACKGROUND: The use of antimicrobials in food animals and the emergence of antimicrobial resistance are global concerns. Ceftiofur is the only third-generation cephalosporin labeled for veterinary use in the USA, and it is the drug of choice in the majority of dairy farms for the treatment of mastitis. Here, we use next-generation sequencing to describe longitudinal changes that occur in the milk microbiome before, during, and after infection and treatment with ceftiofur. Twelve animals were intramammary challenged with Escherichia coli in one quarter and randomly allocated to receive intramammary treatment with ceftiofur (5d) or untreated controls...
July 12, 2017: Microbiome
https://www.readbyqxmd.com/read/28697806/control-of-lupus-nephritis-by-changes-of-gut-microbiota
#12
Qinghui Mu, Husen Zhang, Xiaofeng Liao, Kaisen Lin, Hualan Liu, Michael R Edwards, S Ansar Ahmed, Ruoxi Yuan, Liwu Li, Thomas E Cecere, David B Branson, Jay L Kirby, Poorna Goswami, Caroline M Leeth, Kaitlin A Read, Kenneth J Oestreich, Miranda D Vieson, Christopher M Reilly, Xin M Luo
BACKGROUND: Systemic lupus erythematosus, characterized by persistent inflammation, is a complex autoimmune disorder with no known cure. Immunosuppressants used in treatment put patients at a higher risk of infections. New knowledge of disease modulators, such as symbiotic bacteria, can enable fine-tuning of parts of the immune system, rather than suppressing it altogether. RESULTS: Dysbiosis of gut microbiota promotes autoimmune disorders that damage extraintestinal organs...
July 11, 2017: Microbiome
https://www.readbyqxmd.com/read/28693587/human-presence-impacts-fungal-diversity-of-inflated-lunar-mars-analog-habitat
#13
A Blachowicz, T Mayer, M Bashir, T R Pieber, P De León, K Venkateswaran
BACKGROUND: An inflatable lunar/Mars analog habitat (ILMAH), simulated closed system isolated by HEPA filtration, mimics International Space Station (ISS) conditions and future human habitation on other planets except for the exchange of air between outdoor and indoor environments. The ILMAH was primarily commissioned to measure physiological, psychological, and immunological characteristics of human inhabiting in isolation, but it was also available for other studies such as examining its microbiological aspects...
July 11, 2017: Microbiome
https://www.readbyqxmd.com/read/28693612/genome-resolved-metaproteomic-characterization-of-preterm-infant-gut-microbiota-development-reveals-species-specific-metabolic-shifts-and-variabilities-during-early-life
#14
Weili Xiong, Christopher T Brown, Michael J Morowitz, Jillian F Banfield, Robert L Hettich
BACKGROUND: Establishment of the human gut microbiota begins at birth. This early-life microbiota development can impact host physiology during infancy and even across an entire life span. However, the functional stability and population structure of the gut microbiota during initial colonization remain poorly understood. Metaproteomics is an emerging technology for the large-scale characterization of metabolic functions in complex microbial communities (gut microbiota). RESULTS: We applied a metagenome-informed metaproteomic approach to study the temporal and inter-individual differences of metabolic functions during microbial colonization of preterm human infants' gut...
July 10, 2017: Microbiome
https://www.readbyqxmd.com/read/28683818/longitudinal-profiling-reveals-a-persistent-intestinal-dysbiosis-triggered-by-conventional-anti-tuberculosis-therapy
#15
Sivaranjani Namasivayam, Mamoudou Maiga, Wuxing Yuan, Vishal Thovarai, Diego L Costa, Lara R Mittereder, Matthew F Wipperman, Michael S Glickman, Amiran Dzutsev, Giorgio Trinchieri, Alan Sher
BACKGROUND: Effective treatment of Mycobacterium tuberculosis (Mtb) infection requires at least 6 months of daily therapy with multiple orally administered antibiotics. Although this drug regimen is administered annually to millions worldwide, the impact of such intensive antimicrobial treatment on the host microbiome has never been formally investigated. Here, we characterized the longitudinal outcome of conventional isoniazid-rifampin-pyrazinamide (HRZ) TB drug administration on the diversity and composition of the intestinal microbiota in Mtb-infected mice by means of 16S rRNA sequencing...
July 7, 2017: Microbiome
https://www.readbyqxmd.com/read/28683838/a-novel-ultra-high-throughput-16s-rrna-gene-amplicon-sequencing-library-preparation-method-for-the-illumina-hiseq-platform
#16
Eric J de Muinck, Pål Trosvik, Gregor D Gilfillan, Johannes R Hov, Arvind Y M Sundaram
BACKGROUND: Advances in sequencing technologies and bioinformatics have made the analysis of microbial communities almost routine. Nonetheless, the need remains to improve on the techniques used for gathering such data, including increasing throughput while lowering cost and benchmarking the techniques so that potential sources of bias can be better characterized. METHODS: We present a triple-index amplicon sequencing strategy to sequence large numbers of samples at significantly lower c ost and in a shorter timeframe compared to existing methods...
July 6, 2017: Microbiome
https://www.readbyqxmd.com/read/28683828/virfinder-a-novel-k-mer-based-tool-for-identifying-viral-sequences-from-assembled-metagenomic-data
#17
Jie Ren, Nathan A Ahlgren, Yang Young Lu, Jed A Fuhrman, Fengzhu Sun
BACKGROUND: Identifying viral sequences in mixed metagenomes containing both viral and host contigs is a critical first step in analyzing the viral component of samples. Current tools for distinguishing prokaryotic virus and host contigs primarily use gene-based similarity approaches. Such approaches can significantly limit results especially for short contigs that have few predicted proteins or lack proteins with similarity to previously known viruses. METHODS: We have developed VirFinder, the first k-mer frequency based, machine learning method for virus contig identification that entirely avoids gene-based similarity searches...
July 6, 2017: Microbiome
https://www.readbyqxmd.com/read/28683827/expanding-landscapes-of-the-diversified-mcr-1-bearing-plasmid-reservoirs
#18
Qingjing Wang, Jian Sun, Jun Li, Youfa Ding, Xing-Ping Li, Jingxia Lin, Bachar Hassan, Youjun Feng
BACKGROUND: Polymyxin is a cationic polypeptide antibiotic that can disrupt bacterial cell membrane by interacting with its lipopolysaccharide molecules and is used as a last resort drug against lethal infections by the carbapenem-resistant superbugs (like NDM-1). However, global discovery of the MCR-1 colistin resistance dramatically challenges the newly renewed interest in colistin for clinical use. METHODS: The mcr-1-harboring plasmids were acquired from swine and human Escherichia coli isolated in China, from 2015 to 2016, and subjected to Illumina PacBio RSII and Hi-Seq2000 for full genome sequencing...
July 6, 2017: Microbiome
https://www.readbyqxmd.com/read/28666467/the-metabolic-footprint-of-the-airway-bacterial-community-in-cystic-fibrosis
#19
Vaishnavi Narayanamurthy, John M Sweetnam, Darcy R Denner, Lena W Chen, Edward T Naureckas, Bharathi Laxman, Steven R White
BACKGROUND: Progressive, chronic bacterial infection of the airways is a leading cause of death in cystic fibrosis (CF). Culture-independent methods based on sequencing of the bacterial 16S rRNA gene describe a distinct microbial community that decreases in richness and diversity with disease progression. Understanding the functional characteristics of the microbial community may aid in identifying potential therapies and may assist in management, but current methods are cumbersome. Here, we demonstrate the use of an oxidative metabolic assay as a complement to sequencing methods to describe the microbiome in the airways of patients with CF...
June 30, 2017: Microbiome
https://www.readbyqxmd.com/read/28651630/maternal-inheritance-of-bifidobacterial-communities-and-bifidophages-in-infants-through-vertical-transmission
#20
Sabrina Duranti, Gabriele Andrea Lugli, Leonardo Mancabelli, Federica Armanini, Francesca Turroni, Kieran James, Pamela Ferretti, Valentina Gorfer, Chiara Ferrario, Christian Milani, Marta Mangifesta, Rosaria Anzalone, Moreno Zolfo, Alice Viappiani, Edoardo Pasolli, Ilaria Bariletti, Rosarita Canto, Rosanna Clementi, Marina Cologna, Tiziana Crifò, Giuseppina Cusumano, Sabina Fedi, Stefania Gottardi, Claudia Innamorati, Caterina Masè, Daniela Postai, Daniela Savoi, Massimo Soffiati, Saverio Tateo, Anna Pedrotti, Nicola Segata, Douwe van Sinderen, Marco Ventura
BACKGROUND: The correct establishment of the human gut microbiota represents a crucial development that commences at birth. Different hypotheses propose that the infant gut microbiota is derived from, among other sources, the mother's fecal/vaginal microbiota and human milk. RESULTS: The composition of bifidobacterial communities of 25 mother-infant pairs was investigated based on an internal transcribed spacer (ITS) approach, combined with cultivation-mediated and genomic analyses...
June 26, 2017: Microbiome
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