Human microbiome, June 17

Gut bacteria swapping DNA segments, what happens after a fecal transplant, intestinal archaea, and more.

Gut microbiome

Evidence of Extensive DNA Transfer between Bacteroidales Species within the Human Gut – Michael J. Coyne – mBio

“Using seven coresident Bacteroidales species from one individual and eight from another, we identified five large chromosomal regions, each present in a minimum of three of the coresident strains at near 100% DNA identity.”

Recovery of the Gut Microbiome following Fecal Microbiota Transplantation – Anna M. Seekatz – mBio

“Here we investigated changes in the fecal microbiota structure following FMT in patients with recurrent C. difficile infection, and imputed a hypothetical functional profile based on the 16S rRNA profile using a predictive metagenomic tool.”

The Intestinal Archaea Methanosphaera stadtmanae and Methanobrevibacter smithii Activate Human Dendritic Cells – Corinna Bang – PLOS ONE

“Taken together, our findings strongly argue that the archaeal gut inhabitants M. stadtmanae and M. smithii are specifically recognized by the human innate immune system. “

Microbiota and Metabolome Associated with Immunoglobulin A Nephropathy (IgAN) –
Maria De Angelis – PLOS ONE

“This study aimed at investigating the fecal microbiota, and the fecal and urinary metabolome of non progressor (NP) and progressor (P) patients with immunoglobulin A nephropathy (IgAN). “

Respiratory microbiome

Impact of Experimental Human Pneumococcal Carriage on Nasopharyngeal Bacterial Densities in Healthy Adults – Joshua R. Shak – PLOS ONE

“These data on bacterial associations are the first to be reported surrounding experimental human pneumococcal colonization and show that co-colonizing effects are likely subtle rather than absolute.”

Vaginal microbiome

Diversity and stability of cultured vaginal lactobacilli in pregnant women from a multi-ethnic urban UK population – S.M. Husain – Journal of Applied Microbiology

“Self-collected vaginal swabs at 13 and 20 weeks gestation were obtained from women attending for routine antenatal care and cultured for lactobacilli.”

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Non-human microbiome, June 13

MRSA in cats and dogs, metabolomics on cow rumen, bacteria in soil, sewage and sea water, and how to get rid of invasive species.

Mammal microbiome

Screen Shot 2014-06-13 at 11.26.20 PMCarriage of methicillin-resistant staphylococci by healthy companion animals in the US – J.A. Davis – Letters in Applied Microbiology

“In this study, 276 healthy dogs and cats from veterinary clinics were tested for the presence of antimicrobial-resistant Staphylococcus spp. Isolates were tested for antimicrobial susceptibility and the presence of select resistance genes, and typed using Pulsed-Field Gel Electrophoresis (PFGE).”

Screen Shot 2014-06-13 at 11.29.33 PMMetabolomics analysis reveals large effect of roughage types on rumen microbial metabolic profile in dairy cows – S. Zhao – Letters in Applied Microbiology

“ Rumen fluid was sampled from each cow through a ruminal cannula at 0630 and 1030 h, and the mixed ruminal fluid from 3 day in each cow was analysed using nuclear magnetic resonance (NMR) spectroscopy. A multivariate analysis revealed a significant difference between the ruminal metabolome of the CS and MF groups at both time points. “

Soil microbes

Screen Shot 2014-06-13 at 11.30.13 PMDiversity and activity of sulphur-oxidizing bacteria and sulphate-reducing bacteria in landfill cover soils – F.F. Xia – Letters in Applied Microbiology

“In this study, two landfills with or without landfill gas collection and utilization system were investigated to characterize the role of biotic and abiotic factors affecting diversity and activity of SOB and SRB in the landfill cover soils.”

Water microbes

Screen Shot 2014-06-13 at 11.30.55 PMEvaluation of Bacteroides fragilis GB-124 bacteriophages as novel human-associated faecal indicators in the United States – B.R. McMinn – Letters in Applied Microbiology

“Animal faecal samples (>250) from 14 different species were tested for the presence of the three phage groups. GB-124 phages were consistently detected in sewage (10–102 PFU ml−1), but not in animal faeces.”

Letters in applied microbiologyArcobacter spp. isolated from untreated domestic effluent – J.Y. Merga – Letters in Applied Microbiology

“Arcobacter butzleri and Arcobacter cryaerophilus were isolated from samples of raw untreated domestic sewage influent from nine separate wastewater treatment facilities in Cheshire, UK. This is the first report of Arcobacter spp. from sewage in the UK and suggests that Arcobacter spp. may be present in the human community.”

Sunset beachMarine bacteria could help treat human diseases – Mohamed Hassan – The New Zealand Herald

“New Zealand will take part in the first simultaneous sampling of all the world’s oceans as part of “Micro B3 Ocean Sampling Day” on June 20. The project, at 150 sites worldwide, is spearheaded by Germany’s Jacobs University and the University of Oxford in the UK, and will include researchers from the universities of Auckland and Otago.”

zebra musselBacteria could help kill zebra mussels – Associated Press

“State agricultural officials are reviewing a request from the U.S. Geological Survey to experiment with a bacteria to kill zebra mussels in a northern Wisconsin lake.”

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Human microbiomes, June 6

Bacteria causing IBD (in an animal model), gut microbiota from Spanish infants, and radiation therapy damaging teeth.

Gut microbiome

GutAn intestinal arsonist: pathobiont ignites IBD and flees the scene – Stefan Jellbauer and Manuela Raffatellu – Gut

“Evidence for Proteobacteria as a potential trigger of IBD has been deduced by cohort studies showing that inflammatory diarrhoea caused by either Salmonella species or Campylobacter species predisposes genetically susceptible individuals to developing IBD”

AIEC pathobiont instigates chronic colitis in susceptible hosts by altering microbiota composition – Benoit Chassaing – Gut

“Transient AIEC colonisation, in WT mice, did not alter inflammatory markers, bacterial loads, microbiota composition, nor its pro-inflammatory potential. By contrast, transient AIEC colonisation of T5KO mice drove chronic inflammation which correlated with microbiota components having higher levels of bioactive LPS and flagellin.”

BBAReview: Rapidly expanding knowledge on the role of the gut microbiome in health and disease -M.C. Cénit – Biochimica et Biophysica Acta (BBA) – Molecular Basis of Disease

“In this review we describe the different approaches used to characterize the human microbiome, review current knowledge about the gut microbiome, and discuss the role of gut microbiota in immune homeostasis and autoimmunity.”

Screen Shot 2014-06-07 at 1.49.49 AMEx-Merck exec’s new microbiome startup has a pill that works like a fecal transplant against C. diff – Ransdell Pierson – MedCityNews

“The Seres oral capsule, called SER 109, in early clinical trials quickly eliminated symptoms in more than 90 percent of patients, Pomerantz said in a telephone interview.”

Malnutrition ‘damages gut bacteria’ – BBC Health News

“A team studied the gut health of malnourished children in Bangladesh. Writing in the journal Nature they said the bacterial make-up was not fully restored to normal after food supplements were given.”

Oral microbiome

ToothRadiation therapy alters microhardness and microstructure of enamel and dentin of permanent human teeth – Ligia Maria Napolitano Gonçalves – Journal of Dentistry

“The effects of gamma irradiation on dental substrate might contribute to increased risk of radiation tooth decay associated with salivary changes, microbiota shift and high soft and carbohydrate-rich food intake.”

Pregnancy and Birth

Screen Shot 2014-06-07 at 1.52.06 AMMicrobial Succession in the Gut: Directional Trends of Taxonomic and Functional Change in a Birth Cohort of Spanish Infants – Yvonne Vallès – PLOS Genetics

“Here, we analyze the patterns of taxonomic and functional change in the gut microbiota during the first year of life for a birth cohort of 13 infants. We detect that individual instances of gut colonization vary in the temporal dynamics of microbiota richness, diversity, and composition at both functional and taxonomic levels. “

Probiotics

Screen Shot 2014-06-07 at 1.53.11 AMProbiotics: Separating the Hype From the Healthy – Nikki Fotheringham – HuffingtonPost

“That’s right baby; we’re all just sacks of seething bacteria! Now before you freak out, remember that the word “bacteria” has been given negative connotations by the Purell-fueled paranoia of the germ police. “

 

Metabolomics

Journal of functional foodsStructural features and feruloylation modulate the fermentability and evolution of antioxidant properties of arabinoxylanoligosaccharides during in vitro fermentation by human gut derived microbiota – Jeroen Snelders – Journal of Functional Foods

“Two AXOS samples with a low average degree of arabinose substitution, specifically differing in average degree of polymerization, and three AXOS samples, specifically differing in ferulic acid (FA) content and appearance (free or bound), were incubated with cultured human colon microbiota.”

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