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Microbiome

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https://www.readbyqxmd.com/read/28814344/microbial-phylogeny-determines-transcriptional-response-of-resistome-to-dynamic-composting-processes
#1
Cheng Wang, Da Dong, P J Strong, Weijing Zhu, Zhuang Ma, Yong Qin, Weixiang Wu
BACKGROUND: Animal manure is a reservoir of antibiotic resistance genes (ARGs) that pose a potential health risk globally, especially for resistance to the antibiotics commonly used in livestock production (such as tetracycline, sulfonamide, and fluoroquinolone). Currently, the effects of biological treatment (composting) on the transcriptional response of manure ARGs and their microbial hosts are not well characterized. Composting is a dynamic process that consists of four distinct phases that are distinguished by the temperature resulting from microbial activity, namely the mesophilic, thermophilic, cooling, and maturing phases...
August 16, 2017: Microbiome
https://www.readbyqxmd.com/read/28810907/schr%C3%A3-dinger-s-microbes-tools-for-distinguishing-the-living-from-the-dead-in-microbial-ecosystems
#2
REVIEW
Joanne B Emerson, Rachel I Adams, Clarisse M Betancourt Román, Brandon Brooks, David A Coil, Katherine Dahlhausen, Holly H Ganz, Erica M Hartmann, Tiffany Hsu, Nicholas B Justice, Ivan G Paulino Lima, Julia C Luongo, Despoina S Lymperopoulou, Cinta Gomez-Silvan, Brooke Rothschild-Mancinelli, Melike Balk, Curtis Huttenhower, Andreas Nocker, Parag Vaishampayan, Lynn J Rothschild
While often obvious for macroscopic organisms, determining whether a microbe is dead or alive is fraught with complications. Fields such as microbial ecology, environmental health, and medical microbiology each determine how best to assess which members of the microbial community are alive, according to their respective scientific and/or regulatory needs. Many of these fields have gone from studying communities on a bulk level to the fine-scale resolution of microbial populations within consortia. For example, advances in nucleic acid sequencing technologies and downstream bioinformatic analyses have allowed for high-resolution insight into microbial community composition and metabolic potential, yet we know very little about whether such community DNA sequences represent viable microorganisms...
August 16, 2017: Microbiome
https://www.readbyqxmd.com/read/28807046/a-comprehensive-evaluation-of-the-sl1p-pipeline-for-16s-rrna-gene-sequencing-analysis
#3
Fiona J Whelan, Michael G Surette
BACKGROUND: Advances in next-generation sequencing technologies have allowed for detailed, molecular-based studies of microbial communities such as the human gut, soil, and ocean waters. Sequencing of the 16S rRNA gene, specific to prokaryotes, using universal PCR primers has become a common approach to studying the composition of these microbiota. However, the bioinformatic processing of the resulting millions of DNA sequences can be challenging, and a standardized protocol would aid in reproducible analyses...
August 14, 2017: Microbiome
https://www.readbyqxmd.com/read/28807044/metameta-integrating-metagenome-analysis-tools-to-improve-taxonomic-profiling
#4
Vitor C Piro, Marcel Matschkowski, Bernhard Y Renard
BACKGROUND: Many metagenome analysis tools are presently available to classify sequences and profile environmental samples. In particular, taxonomic profiling and binning methods are commonly used for such tasks. Tools available among these two categories make use of several techniques, e.g., read mapping, k-mer alignment, and composition analysis. Variations on the construction of the corresponding reference sequence databases are also common. In addition, different tools provide good results in different datasets and configurations...
August 14, 2017: Microbiome
https://www.readbyqxmd.com/read/28807017/the-urinary-microbiota-of-men-and-women-and-its-changes-in-women-during-bacterial-vaginosis-and-antibiotic-treatment
#5
Cornelia Gottschick, Zhi-Luo Deng, Marius Vital, Clarissa Masur, Christoph Abels, Dietmar H Pieper, Irene Wagner-Döbler
BACKGROUND: The urinary microbiota is similarly complex as the vaginal and penile microbiota, yet its role as a reservoir for pathogens and for recurrent polymicrobial biofilm diseases like bacterial vaginosis (BV) is not clear. RESULTS: Here, we analysed the urinary microbiota of healthy men and women and compared it with that of women during BV and after antibiotic treatment using next-generation sequencing of the 16S rRNA gene V1-V2 regions. Eight different community types, so called urotypes (UT), were identified in healthy humans, all of which were shared between men and women, except UT 7, dominated in relative abundance by Lactobacillus crispatus, which was found in healthy women only...
August 14, 2017: Microbiome
https://www.readbyqxmd.com/read/28803549/comparative-gut-microbiota-and-resistome-profiling-of-intensive-care-patients-receiving-selective-digestive-tract-decontamination-and-healthy-subjects
#6
Elena Buelow, Teresita D J Bello González, Susana Fuentes, Wouter A A de Steenhuijsen Piters, Leo Lahti, Jumamurat R Bayjanov, Eline A M Majoor, Johanna C Braat, Maaike S M van Mourik, Evelien A N Oostdijk, Rob J L Willems, Marc J M Bonten, Mark W J van Passel, Hauke Smidt, Willem van Schaik
BACKGROUND: The gut microbiota is a reservoir of opportunistic pathogens that can cause life-threatening infections in critically ill patients during their stay in an intensive care unit (ICU). To suppress gut colonization with opportunistic pathogens, a prophylactic antibiotic regimen, termed "selective decontamination of the digestive tract" (SDD), is used in some countries where it improves clinical outcome in ICU patients. Yet, the impact of ICU hospitalization and SDD on the gut microbiota remains largely unknown...
August 14, 2017: Microbiome
https://www.readbyqxmd.com/read/28797298/community-characteristics-of-the-gut-microbiomes-of-competitive-cyclists
#7
Lauren M Petersen, Eddy J Bautista, Hoan Nguyen, Blake M Hanson, Lei Chen, Sai H Lek, Erica Sodergren, George M Weinstock
BACKGROUND: Changes in diet and exercise can alter the gut microbiome of humans and mice; however, few studies to date have assessed the microbiomes of highly fit athletes. In this pilot study, we used metagenomic whole genome shotgun (mWGS) and metatranscriptomic (RNA-Seq) sequencing to show what organisms are both present and active in the gut microbiomes of both professional and amateur level competitive cyclists and to determine if any significant differences exist between these two groups...
August 10, 2017: Microbiome
https://www.readbyqxmd.com/read/28797279/huanglongbing-impairs-the-rhizosphere-to-rhizoplane-enrichment-process-of-the-citrus-root-associated-microbiome
#8
Yunzeng Zhang, Jin Xu, Nadia Riera, Tao Jin, Jinyun Li, Nian Wang
BACKGROUND: Roots are the primary site for plant-microbe interactions. Among the three root-associated layers (i.e., rhizosphere, rhizoplane, and endorhiza), the rhizoplane is a key component serving a critical gating role that controls microbial entry into plant roots. The microbial communities colonizing the three layers are believed to be gradually enriched from the bulk soil inoculum. However, it is unknown how this enrichment process, particularly the rhizosphere to rhizoplane step, is affected by biotic stresses, such as disease...
August 10, 2017: Microbiome
https://www.readbyqxmd.com/read/28793925/perturbed-human-sub-networks-by-fusobacterium-nucleatum-candidate-virulence-proteins
#9
Andreas Zanzoni, Lionel Spinelli, Shérazade Braham, Christine Brun
BACKGROUND: Fusobacterium nucleatum is a gram-negative anaerobic species residing in the oral cavity and implicated in several inflammatory processes in the human body. Although F. nucleatum abundance is increased in inflammatory bowel disease subjects and is prevalent in colorectal cancer patients, the causal role of the bacterium in gastrointestinal disorders and the mechanistic details of host cell functions subversion are not fully understood. RESULTS: We devised a computational strategy to identify putative secreted F...
August 10, 2017: Microbiome
https://www.readbyqxmd.com/read/28793934/statin-therapy-causes-gut-dysbiosis-in-mice-through-a-pxr-dependent-mechanism
#10
Jose A Caparrós-Martín, Ricky R Lareu, Joshua P Ramsay, Jörg Peplies, F Jerry Reen, Henrietta A Headlam, Natalie C Ward, Kevin D Croft, Philip Newsholme, Jeffery D Hughes, Fergal O'Gara
BACKGROUND: Statins are a class of therapeutics used to regulate serum cholesterol and reduce the risk of heart disease. Although statins are highly effective in removing cholesterol from the blood, their consumption has been linked to potential adverse effects in some individuals. The most common events associated with statin intolerance are myopathy and increased risk of developing type 2 diabetes mellitus. However, the pathological mechanism through which statins cause these adverse effects is not well understood...
August 9, 2017: Microbiome
https://www.readbyqxmd.com/read/28793929/shifts-in-coastal-sediment-oxygenation-cause-pronounced-changes-in-microbial-community-composition-and-associated-metabolism
#11
Elias Broman, Johanna Sjöstedt, Jarone Pinhassi, Mark Dopson
BACKGROUND: A key characteristic of eutrophication in coastal seas is the expansion of hypoxic bottom waters, often referred to as 'dead zones'. One proposed remediation strategy for coastal dead zones in the Baltic Sea is to mix the water column using pump stations, circulating oxygenated water to the sea bottom. Although microbial metabolism in the sediment surface is recognized as key in regulating bulk chemical fluxes, it remains unknown how the microbial community and its metabolic processes are influenced by shifts in oxygen availability...
August 9, 2017: Microbiome
https://www.readbyqxmd.com/read/28789710/transplanted-human-fecal-microbiota-enhanced-guillain-barr%C3%A3-syndrome-autoantibody-responses-after-campylobacter-jejuni-infection-in-c57bl-6-mice
#12
Phillip T Brooks, Kelsey A Brakel, Julia A Bell, Christopher E Bejcek, Trey Gilpin, Jean M Brudvig, Linda S Mansfield
BACKGROUND: Campylobacter jejuni is the leading antecedent infection to the autoimmune neuropathy Guillain-Barré syndrome (GBS), which is accompanied by an autoimmune anti-ganglioside antibody attack on peripheral nerves. Previously, we showed that contrasting immune responses mediate C. jejuni induced colitis and autoimmunity in interleukin-10 (IL-10)-deficient mice, dependent upon the infecting strain. Strains from colitis patients elicited T helper 1 (TH1)-dependent inflammatory responses while strains from GBS patients elicited TH2-dependent autoantibody production...
August 8, 2017: Microbiome
https://www.readbyqxmd.com/read/28789705/impact-of-intrapartum-antimicrobial-prophylaxis-upon-the-intestinal-microbiota-and-the-prevalence-of-antibiotic-resistance-genes-in-vaginally-delivered-full-term-neonates
#13
Alicja Nogacka, Nuria Salazar, Marta Suárez, Christian Milani, Silvia Arboleya, Gonzalo Solís, Nuria Fernández, Lidia Alaez, Ana M Hernández-Barranco, Clara G de Los Reyes-Gavilán, Marco Ventura, Miguel Gueimonde
BACKGROUND: Disturbances in the early establishment of the intestinal microbiota may produce important implications for the infant's health and for the risk of disease later on. Different perinatal conditions may be affecting the development of the gut microbiota. Some of them, such as delivery mode or feeding habits, have been extensively assessed whereas others remain to be studied, being critical to identify their impact on the microbiota and, if any, to minimize it. Antibiotics are among the drugs most frequently used in early life, the use of intrapartum antimicrobial prophylaxis (IAP), present in over 30% of deliveries, being the most frequent source of exposure...
August 8, 2017: Microbiome
https://www.readbyqxmd.com/read/28789678/optimization-and-validation-of-sample-preparation-for-metagenomic-sequencing-of-viruses-in-clinical-samples
#14
Dagmara W Lewandowska, Osvaldo Zagordi, Fabienne-Desirée Geissberger, Verena Kufner, Stefan Schmutz, Jürg Böni, Karin J Metzner, Alexandra Trkola, Michael Huber
BACKGROUND: Sequence-specific PCR is the most common approach for virus identification in diagnostic laboratories. However, as specific PCR only detects pre-defined targets, novel virus strains or viruses not included in routine test panels will be missed. Recently, advances in high-throughput sequencing allow for virus-sequence-independent identification of entire virus populations in clinical samples, yet standardized protocols are needed to allow broad application in clinical diagnostics...
August 8, 2017: Microbiome
https://www.readbyqxmd.com/read/28780905/virome-comparisons-in-wild-diseased-and-healthy-captive-giant-pandas
#15
Wen Zhang, Shixing Yang, Tongling Shan, Rong Hou, Zhijian Liu, Wang Li, Lianghua Guo, Yan Wang, Peng Chen, Xiaochun Wang, Feifei Feng, Hua Wang, Chao Chen, Quan Shen, Chenglin Zhou, Xiuguo Hua, Li Cui, Xutao Deng, Zhihe Zhang, Dunwu Qi, Eric Delwart
BACKGROUND: The giant panda (Ailuropoda melanoleuca) is a vulnerable mammal herbivore living wild in central China. Viral infections have become a potential threat to the health of these endangered animals, but limited information related to these infections is available. METHODS: Using a viral metagenomic approach, we surveyed viruses in the feces, nasopharyngeal secretions, blood, and different tissues from a wild giant panda that died from an unknown disease, a healthy wild giant panda, and 46 healthy captive animals...
August 7, 2017: Microbiome
https://www.readbyqxmd.com/read/28768551/feed-additive-probiotics-accelerate-yet-antibiotics-delay-intestinal-microbiota-maturation-in-broiler-chicken
#16
Pengfei Gao, Chen Ma, Zheng Sun, Lifeng Wang, Shi Huang, Xiaoquan Su, Jian Xu, Heping Zhang
BACKGROUND: Reducing antibiotics overuse in animal agriculture is one key in combat against the spread of antibiotic resistance. Probiotics are a potential replacement of antibiotics in animal feed; however, it is not clear whether and how probiotics and antibiotics differ in impact on physiology and microbial ecology of host animals. RESULTS: Host phenotype and fecal microbiota of broilers with either antibiotics or probiotics as feed additive were simultaneously sampled at four time points from birth to slaughter and then compared...
August 3, 2017: Microbiome
https://www.readbyqxmd.com/read/28760163/stable-engraftment-of-human-microbiota-into-mice-with-a-single-oral-gavage-following-antibiotic-conditioning
#17
Christopher Staley, Thomas Kaiser, Lalit K Beura, Matthew J Hamilton, Alexa R Weingarden, Aleh Bobr, Johnthomas Kang, David Masopust, Michael J Sadowsky, Alexander Khoruts
BACKGROUND: Human microbiota-associated (HMA) animal models relying on germ-free recipient mice are being used to study the relationship between intestinal microbiota and human disease. However, transfer of microbiota into germ-free animals also triggers global developmental changes in the recipient intestine, which can mask disease-specific attributes of the donor material. Therefore, a simple model of replacing microbiota into a developmentally mature intestinal environment remains highly desirable...
August 1, 2017: Microbiome
https://www.readbyqxmd.com/read/28738889/influence-of-the-pneumococcal-conjugate-vaccines-on-the-temporal-variation-of-pneumococcal-carriage-and-the-nasal-microbiota-in-healthy-infants-a-longitudinal-analysis-of-a-case-control-study
#18
Moana Mika, Josua Maurer, Insa Korten, Aurélie Allemann, Suzanne Aebi, Silvio D Brugger, Weihong Qi, Urs Frey, Philipp Latzin, Markus Hilty
BACKGROUND: Bacterial colonization of the upper airways is a prerequisite for subsequent invasive disease. With the introduction of the 7- and 13-valent pneumococcal conjugate vaccines (PCV7 and PCV13), changes in pneumococcal upper airway colonization have been described. It is, however, less evident whether the vaccines lead to compositional changes of the upper airway microbiota. Here, we performed a case-control study using samples from a longitudinal infant cohort from Switzerland...
July 24, 2017: Microbiome
https://www.readbyqxmd.com/read/28724443/metagenomics-of-urban-sewage-identifies-an-extensively-shared-antibiotic-resistome-in-china
#19
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
#20
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
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