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Francesca De Filippis, Nicoletta Pellegrini, Luca Laghi, Marco Gobbetti, Danilo Ercolini
BACKGROUND: Diet has a recognized effect in shaping gut microbiota. Many studies link an increase in Prevotella to high-fibre diet, while Bacteroides abundance is usually associated with the consumption of animal fat and protein-rich diets. Nevertheless, closely related species and strains may harbour different genetic pools; therefore, further studies should aim to understand whether species of the same genus are consistently linked to dietary patterns or equally responsive to diet variations...
October 21, 2016: Microbiome
Janine Kamke, Sandra Kittelmann, Priya Soni, Yang Li, Michael Tavendale, Siva Ganesh, Peter H Janssen, Weibing Shi, Jeff Froula, Edward M Rubin, Graeme T Attwood
BACKGROUND: Enteric fermentation by farmed ruminant animals is a major source of methane and constitutes the second largest anthropogenic contributor to global warming. Reducing methane emissions from ruminants is needed to ensure sustainable animal production in the future. Methane yield varies naturally in sheep and is a heritable trait that can be used to select animals that yield less methane per unit of feed eaten. We previously demonstrated elevated expression of hydrogenotrophic methanogenesis pathway genes of methanogenic archaea in the rumens of high methane yield (HMY) sheep compared to their low methane yield (LMY) counterparts...
October 19, 2016: Microbiome
Siddhartha Mandal, Keith M Godfrey, Daniel McDonald, Will V Treuren, Jørgen V Bjørnholt, Tore Midtvedt, Birgitte Moen, Knut Rudi, Rob Knight, Anne Lise Brantsæter, Shyamal D Peddada, Merete Eggesbø
BACKGROUND: Although diet is known to have a major modulatory influence on gut microbiota, knowledge of the specific roles of particular vitamins, minerals, and other nutrients is limited. Modulation of the composition of the microbiota in pregnant women is especially important as maternal microbes are transferred during delivery and initiate the colonization process in the infant. We studied the associations between intake of specific dietary nutrients during pregnancy and gut microbiota composition...
October 19, 2016: Microbiome
Chandan Pal, Johan Bengtsson-Palme, Erik Kristiansson, D G Joakim Larsson
BACKGROUND: Antibiotic resistance genes (ARGs) are widespread but cause problems only when present in pathogens. Environments where selection and transmission of antibiotic resistance frequently take place are likely to be characterized by high abundance and diversity of horizontally transferable ARGs. Large-scale quantitative data on ARGs is, however, lacking for most types of environments, including humans and animals, as is data on resistance genes to potential co-selective agents, such as biocides and metals...
October 7, 2016: Microbiome
Manli Y Davis, Husen Zhang, Lera E Brannan, Robert J Carman, James H Boone
BACKGROUND: Clostridium difficile is the most common known cause of antibiotic-associated diarrhea. Upon the disturbance of gut microbiota by antibiotics, C. difficile establishes growth and releases toxins A and B, which cause tissue damage in the host. The symptoms of C. difficile infection disease range from mild diarrhea to pseudomembranous colitis and toxic megacolon. Interestingly, 10-50 % of infants are asymptomatic carriers of C. difficile. This longitudinal study of the C. difficile colonization in an infant revealed the dynamics of C...
October 7, 2016: Microbiome
Maria Hammond, Felix Homa, Helene Andersson-Svahn, Thijs J G Ettema, Haakan N Joensson
BACKGROUND: Whole genome amplification (WGA) is a challenging, key step in metagenomic studies of samples containing minute amounts of DNA, such as samples from low biomass environments. It is well known that multiple displacement amplification (MDA), the most commonly used WGA method for microbial samples, skews the genomic representation in the sample. We have combined MDA with droplet microfluidics to perform the reaction in a homogeneous emulsion. Each droplet in this emulsion can be considered an individual reaction chamber, allowing partitioning of the MDA reaction into millions of parallel reactions with only one or very few template molecules per droplet...
October 6, 2016: Microbiome
Alessandro Tanca, Antonio Palomba, Cristina Fraumene, Daniela Pagnozzi, Valeria Manghina, Massimo Deligios, Thilo Muth, Erdmann Rapp, Lennart Martens, Maria Filippa Addis, Sergio Uzzau
BACKGROUND: Elucidating the role of gut microbiota in physiological and pathological processes has recently emerged as a key research aim in life sciences. In this respect, metaproteomics, the study of the whole protein complement of a microbial community, can provide a unique contribution by revealing which functions are actually being expressed by specific microbial taxa. However, its wide application to gut microbiota research has been hindered by challenges in data analysis, especially related to the choice of the proper sequence databases for protein identification...
September 27, 2016: Microbiome
Janice Crespo-Salgado, V Matti Vehaskari, Tyrus Stewart, Michael Ferris, Qiang Zhang, Guangdi Wang, Eugene E Blanchard, Christopher M Taylor, Mahmoud Kallash, Larry A Greenbaum, Diego H Aviles
BACKGROUND: End-stage renal disease (ESRD) is associated with uremia and increased systemic inflammation. Alteration of the intestinal microbiota may facilitate translocation of endotoxins into the systemic circulation leading to inflammation. We hypothesized that children with ESRD have an altered intestinal microbiota and increased serum levels of bacterially derived uremic toxins. METHODS: Four groups of subjects were recruited: peritoneal dialysis (PD), hemodialysis (HD), post-kidney transplant and healthy controls...
2016: Microbiome
Weipeng Zhang, Jin Sun, Huiluo Cao, Renmao Tian, Lin Cai, Wei Ding, Pei-Yuan Qian
BACKGROUND: Post-translational modification (PTM) of proteins is one important strategy employed by bacteria for environmental adaptation. However, PTM profiles in deep-sea microbes remain largely unexplored. RESULTS: We provide here insight into PTMs in a hydrothermal vent microbial community through integration of metagenomics and metaproteomics. In total, 2919 unique proteins and 1306 unique PTMs were identified, whereas the latter included acetylation, deamination, hydroxylation, methylation, nitrosylation, oxidation, and phosphorylation...
2016: Microbiome
Heike Margot, Roger Stephan, Taurai Tasara
BACKGROUND: Fresh sprouted seeds have been associated with a number of large outbreaks caused by Salmonella and Shiga toxin-producing E. coli. However, the high number of commensal bacteria found on sprouted seeds hampers the detection of these pathogens. Knowledge about the composition of the sprout microbiome is limited. In this study, the microbiome of mungo bean sprouts and the impact of buffered peptone water (BPW) and Enterobacteriaceae enrichment broth (EE-broth)-based enrichment protocols on this microbiome were investigated...
2016: Microbiome
Robyn Nagel, Rebecca J Traub, Richard J N Allcock, Marcella M S Kwan, Helle Bielefeldt-Ohmann
BACKGROUND: We investigated whether the carriage of Blastocystis in IBS patients was associated with differences in the faecal microbiota. Forty patients with diarrhoea-predominant IBS (26 Blastocystis-positive and 14 Blastocystis-negative) and 57 healthy controls (HC) (42 Blastocystis-positive and 15 Blastocystis-negative) submitted faecal samples for metataxonomic analysis of the 16S ribosomal RNA gene. Differences in the relative abundance of bacteria in these IBS and HC groups were evaluated from phylum to genus level...
2016: Microbiome
Marcus H Y Leung, Kelvin C K Chan, Patrick K H Lee
BACKGROUND: High-throughput sequencing has led to increased insights into the human skin microbiome. Currently, the majority of skin microbiome investigations are limited to characterizing prokaryotic communities, and our understanding of the skin fungal community (mycobiome) is limited, more so for cohorts outside of the western hemisphere. Here, the skin mycobiome across healthy Chinese individuals in Hong Kong are characterized. RESULTS: Based on a curated fungal reference database designed for skin mycobiome analyses, previously documented common skin colonizers are also abundant and prevalent in this cohort...
2016: Microbiome
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No abstract text is available yet for this article.
2016: Microbiome
Jessica J Eichmiller, Matthew J Hamilton, Christopher Staley, Michael J Sadowsky, Peter W Sorensen
BACKGROUND: Although the common, silver, and bighead carps are native and sparsely distributed in Eurasia, these fish have become abundant and invasive in North America. An understanding of the biology of these species may provide insights into sustainable control methods. The animal-associated microbiome plays an important role in host health. Characterization of the carp microbiome and the factors that affect its composition is an important step toward understanding the biology and interrelationships between these species and their environments...
2016: Microbiome
Jacques Ravel, Eric Wommack
The editors of Microbiome would like to thank all our reviewers who have contributed to the journal in 2015.
2016: Microbiome
Mehrbod Estaki, Jason Pither, Peter Baumeister, Jonathan P Little, Sandeep K Gill, Sanjoy Ghosh, Zahra Ahmadi-Vand, Katelyn R Marsden, Deanna L Gibson
BACKGROUND: Reduced microbial diversity in human intestines has been implicated in various conditions such as diabetes, colorectal cancer, and inflammatory bowel disease. The role of physical fitness in the context of human intestinal microbiota is currently not known. We used high-throughput sequencing to analyze fecal microbiota of 39 healthy participants with similar age, BMI, and diets but with varying cardiorespiratory fitness levels. Fecal short-chain fatty acids were analyzed using gas chromatography...
2016: Microbiome
Shira R Abeles, Marcus B Jones, Tasha M Santiago-Rodriguez, Melissa Ly, Niels Klitgord, Shibu Yooseph, Karen E Nelson, David T Pride
BACKGROUND: Antibiotics are a mainstay of treatment for bacterial infections worldwide, yet the effects of typical antibiotic prescriptions on human indigenous microbiota have not been thoroughly evaluated. We examined the effects of the two most commonly prescribed antibiotics (amoxicillin and azithromycin) in the USA to discern whether short-term antibiotic courses may have prolonged effects on human microbiota. RESULTS: We sampled the feces, saliva, and skin specimens from a cohort of unrelated, cohabitating individuals over 6 months...
2016: Microbiome
Alexander G Shaw, Kathleen Sim, Elizabeth Powell, Emma Cornwell, Teresa Cramer, Zoë E McClure, Ming-Shi Li, J Simon Kroll
BACKGROUND: In this manuscript, we investigate the "stones best left unturned" of sample storage and preparation and their implications for the next-generation sequencing of infant faecal microbial communities by the 16S ribosomal ribonucleic acid (rRNA) gene. We present a number of experiments that investigate the potential effects of often overlooked methodology factors, establishing a "normal" degree of variation expected between replica sequenced samples. Sources of excess variation are then identified, as measured by observation of alpha diversity, taxonomic group counts and beta diversity magnitudes between microbial communities...
2016: Microbiome
Francesco Strati, Duccio Cavalieri, Davide Albanese, Claudio De Felice, Claudio Donati, Joussef Hayek, Olivier Jousson, Silvia Leoncini, Massimo Pindo, Daniela Renzi, Lisa Rizzetto, Irene Stefanini, Antonio Calabrò, Carlotta De Filippo
BACKGROUND: The human gut microbiota directly affects human health, and its alteration can lead to gastrointestinal abnormalities and inflammation. Rett syndrome (RTT), a progressive neurological disorder mainly caused by mutations in MeCP2 gene, is commonly associated with gastrointestinal dysfunctions and constipation, suggesting a link between RTT's gastrointestinal abnormalities and the gut microbiota. The aim of this study was to evaluate the bacterial and fungal gut microbiota in a cohort of RTT subjects integrating clinical, metabolomics and metagenomics data to understand if changes in the gut microbiota of RTT subjects could be associated with gastrointestinal abnormalities and inflammatory status...
2016: Microbiome
Alison Morris, Joseph N Paulson, Hisham Talukder, Laura Tipton, Heather Kling, Lijia Cui, Adam Fitch, Mihai Pop, Karen A Norris, Elodie Ghedin
BACKGROUND: Longitudinal studies of the lung microbiome are challenging due to the invasive nature of sample collection. In addition, studies of the lung microbiome in human disease are usually performed after disease onset, limiting the ability to determine early events in the lung. We used a non-human primate model to assess lung microbiome alterations over time in response to an HIV-like immunosuppression and determined impact of the lung microbiome on development of obstructive lung disease...
2016: Microbiome
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