Category Archives: Human oral

Microbiome Digest, October 9, 2014

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Human microbiome general

Advancing the Microbiome Research Community – Curtis Huttenhower – Cell

“We outline opportunities in interdisciplinary research, analytical rigor, standardization, and policy development for this relatively new and rapidly developing field. “

Human oral microbiome

Bioinformatic investigation of the cost management strategies of five oral microbes – K.J. Cross – Molecular Oral Microbiology

“The aim of this study was to investigate if five oral bacterial species implement cost management strategies to reduce the energy burden of extracellular unrecyclable proteins.”

Human skin microbiome

Identification of molecular mechanisms used by Finegoldia magna to penetrate and colonize human skin – Elizabeth C. Murphy – Molecular Microbiology

“This study examines the molecular mechanisms F. magna uses when colonizing or establishing an infection in the skin. “

Human gut microbiome

Bacterial ClpB heat-shock protein, an antigen-mimetic of the anorexigenic peptide α-MSH, at the origin of eating disorders – N Tennoune – Translational Psychiatry

“Here, using proteomics, we identified ClpB heat-shock disaggregation chaperone protein of commensal gut bacteria Escherichia coli as a conformational antigen mimetic of α-MSH.”

Animal models of microbiome research

Effects of essential oil supplementation of a low-energy diet on performance, intestinal morphology and microflora, immune properties and antioxidant activities in weaned pigs – Zhikai Zeng – Animal Science Journal

Soil microbiome

Poster presentation: Starting study of microbial genetics diversity in soils of mangrove preserved in sergipe – Karla Cristina Santos Freire – BMC Proceedings

“This paper proposes the characterization and evaluation of structures and diversity of microbial communities in the soil of mangroves in three conservation areas located in Sergipe.“

Community assembly of ectomycorrhizal fungi along a subtropical secondary forest succession – Cheng Gao – New Phytologist

“We examined the communities of ectomycorrhizal (EM) fungi in young, intermediate and old forests in a Chinese subtropical ecosystem, using 454 pyrosequencing”

Metagenomics / Bioinformatics

Functional phylogenomics analysis of bacteria and archaea using consistent genome annotation with UniFam – Juanjuan Chai – BMC Evolutionary Biology

“A total of 14,727 GenBank prokaryotic genomes were re-annotated using a new protein family database, UniFam, to obtain consistent functional annotations for accurate comparison. “

More Microbiology

Halting harmful helminths – Karl F. Hoffmann, Paul J. Brindley, Matthew Berriman – Science

“More than 300 million people are infected each year with parasitic flatworms such as hydatid tapeworms and blood fluke schistosomes. “

Chromosome position effects on gene expression in Escherichia coli K-12 – Jack A. Bryant – Nucleic Acids Research

“Here, using Escherichia coli K-12, we demonstrate that expression of a reporter gene cassette, comprised of the model E. coli lac promoter driving expression of gfp, varies by ∼300-fold depending on its precise position on the chromosome. “

Microbes in the news

‘Good Poop’ Diet Is the Next Big Thing – Daniela Drake – The Daily Beast

“Now a new book, The Skinny Gut Diet, by nutritionist Brenda Watson, tracks the progress of people who follow a diet specifically designed to alter the gut microbiome. “

Another probiotic advantage: Bacteria protects against heavy metal poisoning – Jim Algar – Tech Times

“Probiotic bacteria found in yogurt can protect people from the effects of exposure to heavy metals, particularly in pregnant women and children, a Canadian study suggests.”

Science, publishing, career

The scientists who get credit for peer review – Richard Van Noorden – Nature

“Publons rewards researchers for putting their peer-review activity online. Nature spoke to the startup’s co-founder and two super-users.”

Meet the New Underclass: People With Ph.D.s in Science – Mark Strauss – iO9

“Once upon a time, newly-minted science Ph.D.s would get research jobs at a senior scientist’s laboratory, to train and hone the ideas they would explore at their own labs. But now the supply of post-doctoral students is outpacing demand, creating a new, hyper-educated underclass.”

Glut of postdoc researchers stirs quiet crisis in science –  Carolyn Y. Johnson – Boston Globe

Japan’s Missing Female Scientists – Jack Grove – Times Higher Education

“Too many female scientists are leaving Japan because they do not feel they can get ahead in its “male-dominated” society, a senior university leader has said.”

Bik’s Picks

Cave paintings change ideas about the origin of art – Pallab Ghosh – BBC

“Researchers tell the journal Nature that the Indonesian discovery transforms ideas about how humans first developed the ability to produce art.”

A timeline of a baby’s first hour – Laura Sanders – Science News

Fired science teacher did not have state license – 9 News

“The teacher fired after his science experiment injured four students, one seriously, did not have a valid Colorado teacher’s license.”

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Human microbiome digest, October 7, 2014

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Treating toxic arsenic levels with yoghurt, colonization patterns in low birthweight infants, evil alliances in breastmilk, and smoking and oral microbiome.

Human microbiome general

Opinion: Conservation and stewardship of the human microbiome – Kieran C. O’Doherty – PNAS USA

“Just as humans have impacted many large animal species in the environment, drastic changes in human lifestyle over the past century may have altered the global pool of human-associated microbes; if so, these shifts may pose substantial threats to individual and public health.”

Friends with Social Benefits: Host-Microbe Interactions as a Driver of Brain Evolution and Development? – Roman M. Stilling – Frontiers in Cellular and Infection Microbiology

“Here in this hypothesis and theory article, we propose how host-microbe associations potentially influenced mammalian brain evolution and development. “

Pregnancy and birth

Intestinal Colonization Among Very Low Birth Weight Infants in First Week of Life (PDF) – Sourabh Dutta – Indian Pediatrics

“Very low birth weight infants admitted in neonatal intensive care units have abnormal intestinal colonization patterns”

Is a fetus developing in a sterile environment? – Trudy M. Wassenaar and Pinaki Panigrahi – Letters in Applied Microbiology

Probiotics and Necrotizing Enterocolitis – Josef Neu – Clinics in Perinatology (paywalled even at Stanford)

Potential involvement of Campylobacter curvus and Haemophilus parainfluenzae in preterm birth – George Louis Mendz – BMJ Case Reports

“A woman presented with prelabour premature preterm rupture of membranes and delivered extremely preterm at 26 weeks by caesarean section.”

Network analysis reveals a potentially ‘evil’ alliance of opportunistic pathogens inhibited by a cooperative network in human milk bacterial communities – Zhanshan Ma – arXiv

“..we reconstructed a milk bacterial community network with the data from Hunt et al (2011), which is the largest 16S-rRNA sequence data set of human milk microbiome available to date.”

Randomized Open-Label Pilot Study of the Influence of Probiotics and the Gut Microbiome on Toxic Metal Levels in Tanzanian Pregnant Women and School Children – Jordan E. Bisanz – mBio

“Consumption of probiotic yogurt had a protective effect against further increases in mercury (3.2 nmol/liter; P = 0.035) and arsenic (2.3 nmol/liter; P = 0.011) blood levels in the pregnant women, but this trend was not statistically significant in the children.”

Human oral microbiome

* Alcohol and tobacco consumption affects bacterial richness in oral cavity mucosa biofilms – Andrew Maltez Thomas – BMC Microbiology

“DNA was extracted from swabs and the V1 region of the 16S rRNA gene was PCR amplified and sequenced using the Ion Torrent PGM platform, generating 3.7 million high quality reads. “

* Subgingival microbiome in smokers and non-smokers in Korean chronic periodontitis patients – Ji-Hoi Moon – Molecular Oral Microbiology

“Here, we investigated the composition of subgingival bacterial communities from the pooled plaque samples of smokers and non-smokers, 134 samples each group, in Korean moderate chronic periodontitis patients using 16S rRNA gene-based pyrosequencing.”

Human respiratory microbiome

Sinus culture poorly predicts resident microbiota – Leah J. Hauser – International Forum of Allergy & Rhinology

“The association between 16S relative abundance and detection by culture was determined using logistic regression.”

Localization of Burkholderia cepacia Complex Bacteria in Cystic Fibrosis Lungs and Interactions with Pseudomonas aeruginosa in Hypoxic Mucus – Ute Schwab – Infection and Immunity

“We performed immunohistochemistry for Bcc and P. aeruginosa bacteria on 21 coinfected or singly infected CF lungs obtained at transplantation or autopsy. “

Human gut microbiome

* Intestinal permeability, gut-bacterial dysbiosis, and behavioral markers of alcohol-dependence severity – Sophie Leclercq – PNAS USA

“In this study, we showed that alcohol-dependent subjects with altered intestinal permeability had also altered gut-microbiota composition and activity and remained with high scores of depression, anxiety, and alcohol craving after a short-term detoxification program.”

Structural modulation of gut microbiota during alleviation of type 2 diabetes with a Chinese herbal formula – Jia Xu – ISME Journal

“Pyrosequencing of the V3 regions of 16S rRNA genes revealed a dose-dependent deviation of gut microbiota in response to GQD treatment.”

Modelling the emergent dynamics and major metabolites of the human colonic microbiota – Helen Kettle – Environmental Microbiology

“To reduce the complexity of the system, we divide the bacterial community into 10 bacterial functional groups (BFGs) each distinguished by its substrate preferences, metabolic pathways and its preferred pH range. “

Animal models of microbiome research

Transcriptome analysis of Escherichia coli O157:H7 grown in vitro in the sterile-filtrated cecal content of human gut microbiota associated rats reveals an adaptive expression of metabolic and virulence genes – Guillaume Le Bihan – Microbes and Infection

“A transcriptomic analysis was performed on the EHEC strain EDL933 incubated in vitro in the sterile-filtrated cecal content of human microbiota-associated rats (HMC) compared with EDL933 incubated in the sterile-filtrated cecal content of germ-free rat (GFC).”

Early Innate Immunity to Bacterial Infection in the Lung Is Regulated Systemically by the Commensal Microbiota via Nod-Like Receptor Ligands – Thomas B. Clarke – Infection and Immunity

“Microbiota depletion caused significant defects in the early innate response to lung infection by the major human pathogen Klebsiella pneumoniae.”

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Human microbiome digest, October 2, 2014

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Catching up after some long days of paper writing. Lots of microbiome papers in the Journal of Clinical Investigation, microbiome and Lupus, and biography of skin microbiome.

General (human) microbiome

The Journal of Clinical Investigation has a microbiome issue this month (all behind a subscription wall). Titles include:

The microbiome revolution – Martin J. Blaser
Bacteroides fragilis subverts mucosal biology: from symbiont to colon carcinogenesis – Cynthia L. Sears, Abby L. Geis, Franck Housseau
Host-microbial interactions in the metabolism of therapeutic and diet-derived xenobiotics – Rachel N. Carmody, Peter J. Turnbaugh
Clostridium difficile and the microbiota – Anna M. Seekatz, Vincent B. Young
The microbial basis of inflammatory bowel diseases – Sushila R. Dalal, Eugene B. Chang
Deciphering the tête-à-tête between the microbiota and the immune system – Neeraj K. Surana, Dennis L. Kasper
The contributory role of gut microbiota in cardiovascular disease – W.H. Wilson Tang, Stanley L. Hazen
Antibiotics and the gut microbiota – Sheetal R. Modi, James J. Collins, David A. Relman

When, where and how does microbial community composition matter? – Diana R. Nemergut*, Ashley Shade and Cyrille Violle – Frontiers in Microbiology

“Several papers in this special issue, “The Causes and Consequences of Microbial Community Structure,” use empirical or modeling approaches as well as literature reviews to enrich our mechanistic understanding of the controls over the relationship between community structure and ecosystem processes. “

The bacteriome-mycobiome interaction and antifungal host defense – Jaap ten Oever and Mihai G. Netea – European Journal of Immunology

“In this review, we describe the role of the bacterial microbiome in antifungal host defense.”

Richness and diversity of mammalian fungal communities shape innate and adaptive immunity in health and disease – Lisa Rizzetto – European Journal of Immunology

“In this review, we describe the ecology and the human niches of our fungal “fellow travelers” in both health and disease, discriminating between passengers, colonizers and pathogens based on the interaction of these fungi with the human immune system.”

Pregnancy and Birth

Second trimester amniotic fluid cytokine concentrations, Ureaplasma sp. colonisation status and sexual activity as predictors of preterm birth in Chinese and Australian women
Matthew S Payne – BMC Pregnancy and Childbirth

“Second trimester amniocentesis for measurement of inflammatory markers and Ureaplasma sp. DNA was not indicative of risk of preterm birth, at least in these populations.”

Human oral microbiome

Tongue images and tongue coating microbiome in patients with Colorectal Cancer -Shuwen Han – Microbial Pathogenesis

“To evaluate the differences of tongue images and tongue coating microbiome between patients with colorectal cancer and healthy people.”

Hydrogen Sulfide Production from subgingival plaque samples – A. Basic, G. Dahlén – Anaerobe

“The Karen population studied in Northern Thailand showed poor oral hygiene, general gingivitis and moderate periodontal destruction and little tooth loss.”

Italian-style gluten-free diet changes the salivary microbiota and metabolome of African (Saharawi) celiac children – Ruggiero Francavilla – Digestive and Liver Disease

Human skin microbiome

* Microbiology: An integrated view of the skin microbiome – Patrick D. Schloss – Nature

Biogeography and individuality shape function in the human skin metagenome – Julia Oh – Nature

“Here metagenomic analyses of diverse body sites in healthy humans demonstrate that local biogeography and strong individuality define the skin microbiome. “

Human respiratory microbiome

Sinus culture poorly predicts resident microbiota – Leah J. Hauser – International Forum of Allergy & Rhinology

“Ethmoid samples from 54 CRS patients collected during endoscopic sinus surgery were analyzed by both clinical culture and 16S ribosomal RNA (rRNA) gene sequencing. The association between 16S relative abundance and detection by culture was determined using logistic regression.”

Methicillin-Sensitive and Methicillin-Resistant Staphylococcus aureus Nasal Carriage in a Random Sample of Non-Hospitalized Adult Population in Northern Germany – Jaishri Mehraj – PLOS ONE

“A total of 2026 potential participants were randomly selected through the resident’s registration office and invited by mail. They were requested to collect a nasal swab at home and return it by mail. S. aureus was identified by culture and PCR. “

Severity-related changes of bronchial microbiome in COPD – Marian Garcia-Nunez – Journal of Clinical Microbiology

“Bronchial microbiome of COPD patients was analyzed by 16S rRNA gene amplification and pyrosequencing in sputum samples obtained during stability. “

Human gut microbiome

* Intestinal Dysbiosis Associated with Systemic Lupus Erythematosus – Arancha Hevia – mBio

“A group of 20 SLE patients in remission, for which there was strict inclusion and exclusion criteria, was recruited, and we used an optimized Ion Torrent 16S rRNA gene-based analysis protocol to decipher the fecal microbial profiles of these patients and compare them with those of 20 age- and sex-matched healthy control subjects.”

Systems Biology Analysis of Omeprazole Therapy in Cirrhosis Demonstrates Significant Shifts in Gut Microbiota Composition and Function – Jasmohan Singh Bajaj- American Journal of Physiology – Gastrointestinal and Liver Physiology

“15 compensated cirrhotics and 15 age-matched controls underwent serum gastrin measurement, stool microbiota profiling with multi-tagged pyrosequencing and urinary metabolic profiling with NMR spectroscopy to assess microbial co-metabolites before/after a 14-day course of 40mg/day omeprazole under constant diet conditions’

The Impact of Proton Pump Inhibitors on the Human Gastrointestinal Microbiome
Daniel E. Freedberg – Clinics in Laboratory Medicine

The intestinal microbiota and allergic asthma – Marie-Claire Arrietaa, Brett Finlay- Journal of Infection

“By describing some of the most relevant human and animal studies in this field, we explore the concept that significant perturbations of the intestinal and perhaps the lung microbiota are a cause of allergic asthma.”

Minireview: Linking genetic variation in human Toll-like receptor 5 genes to the gut microbiome’s potential to cause inflammation – Cynthia A. Leifer – Immunology Letters

“Loss of TLR5 has profound effects on the microbiota that include greater temporal instability of major lineages and upregulation of flagellar motility genes that may be linked to the reduced levels of anti-flagellin antibodies in the TLR5-/- host.”

A Little O2 May Go a Long Way in Structuring the GI Microbiome – Thomas M. Schmidt, John Y. Kao – Gastroenterology

Microbiome, Innate Immunity, and Esophageal Adenocarcinoma – Jonathan Baghdadi – Clinics in Laboratory Medicine

Animal models of microbiome research

Immunology: Starve a fever, feed the microbiota – Seth Rakoff-Nahoum & Laurie E. Comstock – Nature – belongs to:

Rapid fucosylation of intestinal epithelium sustains host–commensal symbiosis in sickness – Joseph M. Pickard – Nature

“We hypothesized that the host might utilize internal resources to support the gut microbiota during the acute phase of the disease.”

Bacteria from Diverse Habitats Colonize and Compete in the Mouse Gut – Henning Seedorf – Cell

“Microbiota from diverse habitats colonize and compete in the guts of gnotobiotic mice”

Dynamics of gut microbiota in autoimmune lupus – Husen Zhang – Applied and Environmental Microbiology

“We investigated the effects of host genetics, sex, age, and dietary intervention on the gut microbiome in a murine lupus model.”

Clostridium ramosum Promotes High-Fat Diet-Induced Obesity in Gnotobiotic Mouse Models – Anni Woting – mBio

“To clarify the possible obesogenic potential of this bacterial species and to unravel the underlying mechanism, we investigated the role of C. ramosum in obesity development in gnotobiotic mice.”

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Human microbiome digest, September 29, 2014

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Smoking and the subgingival ecosystem, inflammatory bowel diseases, iron in the gut, and metabolism of acetaminophen.

Pregnancy and birth

External influence of early childhood establishment of gut microbiota and subsequent health implications – Peris M. Munyaka – Frontiers in Pediatrics

“Early exposures impacting the intestinal microbiota are associated with the development of childhood diseases that may persist to adulthood”

Human oral microbiome

* Smoking decreases structural and functional resilience in the subgingival ecosystem – Vinayak Joshi – Journal of Clinical Periodontology

“16S cloning and sequencing was used for bacterial identification and multiplexed bead-based flow cytometry was used to quantify the levels of 27 immune mediators.”

Human gut microbiome

Functional Impacts of the Intestinal Microbiome in the Pathogenesis of Inflammatory Bowel Disease – Jennifer Li – Inflammatory Bowel Diseases

“We highlight functional roles of specific bacterial groups in the development and management of IBD. “

Nutritional iron turned inside out: intestinal stress from a gut microbial perspective – Guus A.M. Kortman – FEMS Microbiology Reviews

“This review covers the multifaceted aspects of nutritional iron stress with respect to growth, composition, metabolism and pathogenicity of the gut microbiota in relation to human health.”

Animal models of microbiome research

The role of intestinal microbiota in murine models of acetaminophen-induced hepatotoxicity – Lucia A Possamai – Liver International

“A urinary metabolic profile was obtained using 1H-NMR. Baseline hepatic glutathione content and CYP2E1 expression were quantified.”

Dietary Xylo-oligosaccharide stimulates intestinal bifidobacteria and lactobacilli but has limited effect on intestinal integrity in rats – Ellen Gerd Christensen – BMC Research Notes

“Changes in faecal and caecal bacterial composition determined by 16S rRNA gene sequencing and quantitative PCR for selected bacterial groups revealed that the overall bacterial composition did not differ markedly“

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Microbiome digest, September 22, 2014

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Temporal stability of the microbiomes of 85 adults, bacteria in breast milk, vaginal microbiome during pregnancy, water microbiomes, and Bik’s Picks.

Human microbiome general

Temporal variability is a personalized feature of the human microbiome – Gilberto E Flores – PeerJ PrePrints

“Here we address this gap in understanding by profiling the forehead, gut (fecal), palm, and tongue microbial communities in 85 adults, weekly over three months.”

Pregnancy and birth

It’s Alive: Microbes and Cells in Human Milk and Their Potential Benefits to Mother and Infant – Lars Bode – Advances in Nutrition

“This article is a summary of the symposium “It’s Alive: Microbes and Cells in Human Milk and Their Potential Benefits to Mother and Infant” held 29 April 2014 at the ASN Scientific Sessions and Annual Meeting at Experimental Biology 2014 in San Diego, CA.”

Microorganisms in the Female Genital Tract during Pregnancy: Tolerance versus Pathogenesis – Bruna de Andrade Ramos – American Journal of Reproductive Immunology

“We review the state of knowledge of microbe–host interactions in gestational tissues and highlight mechanisms that promote tolerance or pathogenesis.”

Determinants and pattern of care seeking for preterm newborns in a rural Bangladeshi cohort – Rashed Shah – BMC Health Services Research

“Only one-fifth (19.7%) of preterm newborns were taken to seek either preventive or curative health care.”

Human oral microbiome

Microbial signature profiles of periodontally healthy and diseased patients – Talita Gomes Baêta Lourenço – Journal of Clinical Periodontology

“Subgingival biofilm was obtained from patients with periodontal health (27), gingivitis (11), chronic periodontitis (35) and aggressive periodontitis (24), and analysed for the presence of >250 species/phylotypes using HOMIM.”

Human gut microbiome

Review: Modulation of the Gut Microbiota by Nutrients with Prebiotic and Probiotic Properties – Céline Druart – Advances in Nutrition

“In this review, we describe how changes in the composition and/or activity of the gut microbiota by administration of nutrients with probiotic or prebiotic properties can modulate host gene expression and metabolism and thereby positively influence host adipose tissue development and related metabolic disorders.”

Mammal microbiome

Resistance to Antibiotics of Clinical Relevance in the Fecal Microbiota of Mexican Wildlife – Jurgi Cristóbal-Azkarate – PLOS ONE

“Here, we used culture and molecular methods to assess ATBR in bacteria in fecal samples from howler monkeys, spider monkeys, tapirs and felids living freely in two regions of the Mexican state of Veracruz under different degrees of human influence.“

Bird microbiome

Do feather-degrading bacteria actually degrade feather colour? No significant effects of plumage microbiome modifications on feather colouration in wild great tits – Staffan Jacob – Naturwissenschaften

“Here, we tested whether (i) keratinolytic microorganisms can degrade feathers in vivo and thus modify the colour of feathers during the nesting period and (ii) whether feather microorganisms have a long-term effect on the investment in colouration of newly moulted feathers.”

Plant microbiome

Impact of swapping soils on the endophytic bacterial communities of pre-domesticated, ancient and modern maize – David Johnston-Monje – BMC Plant Biology

“The impact of these soil swaps on founder bacterial endophyte communities was tested using 16S-rDNA profiling, culturing and microbial trait phenotyping.“

Microbiota in Wheat Roots, Rhizosphere and Soil in Crops Grown in Organic and Other Production Systems – Leszek Lenc – Journal of Phytopathology

“The other two systems were intermediate, with microbial communities suggesting that the conventional system produced a slightly more suppressive environment than the integrated system. “

Soil microbiome

Bacterial and Archaeal Communities in Bleached Mottles of Tropical Podzols –
K. J. Silva, P. Vidal-Torrado, M. R. Lambais – Microbial Ecology

“In this study, we examined the bacterial and archaeal communities along three Brazilian coastal podzol profiles, as well as in bleached mottles and their immediate vicinity, using 16S rRNA gene profiling.”

Water microbiome

Microplastic is an abundant and distinct microbial habitat in an urban river – Amanda McCormick – Environmental Science & Technology

“Results from high-throughput sequencing showed that bacterial assemblages colonizing microplastic within the river were less diverse and were significantly different in taxonomic composition compared to those from the water column and suspended organic matter.”

Application of Ion Torrent Sequencing to the Assessment of the Effect of Alkali Ballast Water Treatment on Microbial Community Diversity – Masanori Fujimoto – PLOS ONE

“The impact of NaOH as a ballast water treatment (BWT) on microbial community diversity was assessed using the 16S rRNA gene based Ion Torrent sequencing with its new 400 base chemistry.”

Microbial diversity of the Soldhar hot spring, India, assessed by analyzing 16S rRNA and protein-coding genes – Avinash Sharma – Annals of Microbiology

“Bacterial diversity of the Soldhar hot spring, located in the Chamoli district of Uttarakhand, India, was investigated using a clone library, denaturing gradient gel electrophoresis (DGGE) and functional genes.”

Microbial community composition and in silico predicted metabolic potential reflect biogeochemical gradients between distinct peatland types – Zuzana Urbanová and Jiří Bárta – FEMS Microbial Ecology

“Species richness and microbial diversity increased significantly from bog to fen, with SSF in between, reflecting the variation in pH, nutrient availability and peat decomposability. “

A molecular survey of freshwater microeukaryotes in an Arctic reservoir (Svalbard, 79°N) in summer by using next-generation sequencing – Thangavelu Boopathi – Polar Biology

“In this study, freshwater microeukaryotes in an Arctic reservoir at Ny-Ǻlesund (Svalbard, Norway) were studied using the hypervariable V1–V3 small subunit rRNA and 454 pyrosequencing.”

Built Environment

Urban microbiomes and urban ecology: How do microbes in the built environment affect human sustainability in cities? – Gary M. King – Journal of Microbiology

“I provide here a definition of the urban microbiome, and through examples indicate its centrality to human function and wellbeing in urban systems”

Phages and viruses

Metagenomic Evaluation of the Highly Abundant Human Gut Bacteriophage CrAssphage for Source Tracking of Human Fecal Pollution – Elyse Stachler and Kyle Bibby – Environmental Science & Technology

“Here, 86 publically available metagenomes were surveyed to determine the presence and abundance of crAssphage in various environments, and to identify its utility for source tracking of human fecal pollution.”

Microbes in the news

Understanding the Microbiome and Its Impact on Human Health – Kristine Nally – HCPLive

“Instant polling at an educational session of the 2014 American Academy of Pain Management annual clinical meeting in Phoenix, AZ, revealed that only 40 percent of the approximately 350-person audience was “familiar” with the concept of a microbiome.”

Mining the microbiome for medicines – Set a thief… – The Economist

“Antibiotics are not the only things Dr Donia’s technique might turn up, for the bugs in the human microbiome spit out all sorts of other chemicals that could potentially be put to use as drugs.”

Techniques

Comparative Analysis of Functional Metagenomic Annotation and the Mappability of Short Reads – Rogan Carr and Elhanan Borenstein – MicroBEnet

“We therefore set out to develop a set of ‘best practices’ for our lab for metagenomic sequence annotation and to prove (or disprove) quantitatively that such direct functional annotation of short reads provides a valid functional representation of the sample.”

Science and publishing

Anonymous peer-review comments may spark legal battle – Kelly Servick – Science Insider

“The power of anonymous comments—and the liability of those who make them—is at the heart of a possible legal battle embroiling PubPeer, an online forum launched in October 2012 for anonymous, postpublication peer review.”

Time to Raise the Profile of Women and Minorities in Science – Brian Welle and Megan Smith – Scientific American

“Along these lines, over the past few years, we discovered some pretty ugly news about our beloved Google Doodles. “

Bik’s Picks

Immune system of newborn babies stronger than previously thought – Science Daily

“Contrary to what was previously thought, newborn immune T cells may have the ability to trigger an inflammatory response to bacteria, according to a new study.”

The Preservation Of Lonesome George – Sarah Fecht – PopSci.com

“Decades after the last giant tortoise was thought to have disappeared from the island of Pinta in the Galapagos, Lonesome George turned up in 1971 and became a conservation icon.”

 Great white sharks partly to blame for otter recovery stall – Peter Fimrite – SF Gate

“Most scientists agree that the number of animals, which are also known as southern sea otters, should be increasing, but hungry predators and a lack of food may be limiting their growth.”

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Microbiome digest, September 19, 2014

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An update from the Cochrane Review Journal on probiotics to prevent necrotizing enterocolitis, oral microbiome in apical periodontitis or polycystic ovary syndrome, vaginal and gut microbiome, and bacteria in shrimp, soil, and water.
Pregnancy and birth

Probiotics for prevention of necrotizing enterocolitis in preterm infants – Khalid AlFaleh, and Jasim Anabrees – Evidence-Based Child Health: A Cochrane Review Journal

“For this update, searches were made of MEDLINE (1966 to October 2013), EMBASE (1980 to October 2013), the Cochrane Central Register of Controlled Trials (CENTRAL) in The Cochrane Library (2013, Issue 10), and abstracts of annual meetings of the Society for Pediatric Research (1995 to 2013).”

Anne Geddes Unveils New Image Of A Baby Born Too Soon – March of Dimes

“Mrs. Geddes donated the image of Alfred, who was born 8 weeks too soon, weighing just two pounds, six ounces, to the March of Dimes, which made the photo the center of its 2014 World Prematurity Day campaign.”

Human oral microbiome

Highly Diverse Microbiota in Dental Root Canals in Cases of Apical Periodontitis (Data of Illumina Sequencing) – Veiko Vengerfeldt – Journal of Endodontics

“Samples were collected under strict aseptic conditions from 12 teeth … and characterized by profiling the microbial community on the basis of the V6 hypervariable region of the 16S ribosomal RNA gene by using Illumina HiSeq2000 sequencing combinatorial sequence-tagged polymerase chain reaction products.”

Association between Polycystic Ovary Syndrome, Oral Microbiota and Systemic Antibody Responses – Aliye Akcalı – PLOS ONE

“Salivary levels of seven putative periodontal pathogens were analyzed by quantitative real-time polymerase chain reaction and serum antibody levels were analyzed by ELISA. “

Human genital microbiome

The Changing Landscape of the Vaginal Microbiome – Bernice Huang – Clinics in Laboratory Medicine

“The vaginal microbiome is a dynamic ecosystem in which the microbiota play a major role in regulating parameters such as pH and in limiting the growth of potentially harmful organisms”

Human gut microbiome

Review: Diet, gut microbes, and genetics in immune function: can we leverage our current knowledge to achieve better outcomes in inflammatory bowel diseases? – Vanessa A Leone – Current Opinion in Immunology

“This review summarizes our current understanding of dietary-induced changes in gut microbiota on autoimmunity in the context of IBD.”

The evolving role of the gut microbiome in human disease – Lloyd H. Kasper – FEBS Letters

“We are delighted to introduce this Special Issue, which summarizes the current understanding of the complex relationship between the gut microbiome and the host.”

Virulence genes are a signature of the microbiome in the colorectal tumor microenvironment – Michael B Burns – bioRxiv Preprints

“We characterized the microbiome in 44 primary tumor and 44 patient-matched normal colon tissues. We find that tumors harbor distinct microbial communities compared to nearby healthy tissue.”

Gut Microbiota: A Natural Adjuvant for Vaccination – Oliver Pabst, Mathias Hornef – Immunity

“In this issue of Immunity, Oh et al. (2014) reveal an unappreciated facet of how the microbiota influences immune responses. Immunity to nonadjuvanted vaccines depends on Toll-like-receptor-5-mediated sensing of the microbiota.”

Animal and bioreactor models

TLR5-Mediated Sensing of Gut Microbiota Is Necessary for Antibody Responses to Seasonal Influenza Vaccination – Jason Z. Oh – Immunity

“Vaccination of Trl5−/− mice resulted in reduced antibody titers and lower frequencies of plasma cells, demonstrating a role for TLR5 in immunity to TIV. This was due to a failure to sense host microbiota. “

In vivo degradation of alginate in the presence and in the absence of resistant starch – Melliana Jonathan – Food Chemistry

“This study evaluated the intestinal degradability of alginate during 74 days intake in pigs as models for humans. “

Effect of prebiotics on the fecal microbiota of elderly volunteers after dietary supplementation of Bacillus coagulans GBI-30, 6086 – Edna P. Nyangale – Anaerobe

“Single stage batch culture anaerobic fermenters were used and inoculated with fecal microbiota obtained from volunteers after taking a 28 day treatment of Bacillus coagulans GBI-30, 6086 (GanedenBC30 (BC30)) or a placebo.”

Intestinal anastomotic injury alters spatially defined microbiome composition and function – Benjamin D Shogan – Microbiome journal

“Using 16S rRNA amplicon sequencing of samples collected on the day of surgery … and the 6th day following surgery …, we analyzed the changes in luminal versus tissue-associated microbiota at anastomotic sites created in the colon of rats.”

General human microbiome

Microbiome in Human Immunodeficiency Virus Infection – January T. Salas, Theresa L. Chang – Clinics in Laboratory Medicine

“Individuals infected with the human immunodeficiency virus (HIV) have altered microbiome associated with immune activation that impacts the consquence of disease progression”

Shrimp microbiome

Characterization of the intestinal microbiota in Pacific white shrimp, Litopenaeus vannamei, fed diets with different lipid sources – Meiling Zhang – Aquaculture

“an Illumina-based sequencing method was used to examine the intestinal bacterial composition of L. vannamei following six diets with different lipid sources.”

Soil microbiome

Pyrosequencing reveals the effect of mobilizing agents and lignocellulosic substrate amendment on microbial community composition in a real industrial PAH-polluted soil –
S. Lladó – Journal of Hazardous Materials

“Soil microbial community assessment through classical (MPN) and molecular tools (DGGE and pyrosequencing) is provided”

Water microbiome

High-throughput sequencing reveals neustonic and planktonic microbial eukaryote diversity in coastal waters – Joe D. Taylor and Michael Cunliffe – Journal of Phycology

“Here, we use high-throughput 18S rRNA gene sequencing to characterize protist and fungal diversity in the SML at a coastal time-series station and compare with underlying plankton assemblages. “

Microbes in the news

Sex in the Sink: Gene-Swapping Bacteria Are Making New Superbugs – Maggie Fox – NBC News

“Over the past decade, there has been a steady and alarming increase in antibiotic-resistant bacteria, a trend that poses a serious threat to the U.S. medical system,” Segre and colleagues wrote in their report.

Science, publishing, and career

To Get More Out of Science, Show the Rejected Research – Brendan Nyhan – New York Times

“In a new white paper, I propose that the American Political Science Association offer options for articles in a Registered Reports-style format. “

Pushing Women and People of Color Out of Science Before We Go In – Jennifer Selvidge – Huffington Post

“The misogyny and racism I experienced and saw at MIT became more and more concerning, between professors making “get back in the kitchen jokes” and hearing about what seemed to be legions of male PhD student sexually harassing woman undergraduates.”

Bik’s Picks

I want one! These adorable giant African rats detect land mines and TB for a living – Bec Crew – Scientific American

“So yesterday, I adopted an unborn land-mine-detecting African giant pouched rat (Cricetomys gambianus) from Tanzania. “

No sedative necessary: Scientists discover new ‘sleep node’ in the brain – Science Daily

“A sleep-promoting circuit located deep in the primitive brainstem has revealed how we fall into deep sleep. “

Experts: Science Class Can Dazzle With Less Danger – Dan Elliott – ABC News

“On Sept. 3, 13 people, mostly children, were burned by a methanol-fueled flash fire during a science demonstration at the Terry Lee Wells Nevada Discovery Museum in Reno.”

(Satire) Bono Showcases New Genome Sequencers, The i-LUMINA 6 and i-LUMINA 6 plus – the Allium

“Lead singer with the rock band U2, Bono, revealed the latest in genome sequencing technology at a gala event in the Moscone Center in San Francisco, yesterday.”

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Human microbiome digest, September 16, 2014

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Still catching up after my vacation, but almost there!

Some general microbiome reviews, using saliva to track human evolution, probiotics that actually change the microbiome, and several animal model studies.

 

General microbiome reviews

Which is more important for classifying microbial communities: who’s there or what they can do? – Zhenjiang Xu – ISME Journal

“… might we not instead expect that function would be substantially more important for classifying biologically meaningful groups of samples than who is providing those functions? “

Microbiome analysis – from technical advances to biological relevance – Michelle I. Smith – F1000Prime Reports

“Here, we introduce techniques that go beyond identifying the taxa present within a sample and examine the biological function of the microbiome or the host-microbiome interaction.”

From barcoding single individuals to metabarcoding biological communities: towards an integrative approach to the study of global biodiversity – Melania E. Cristescu – Trends in Ecology & Evolution

“DNA-based species identification, known as barcoding, transformed the traditional approach to the study of biodiversity science. “

Human oral microbiome

Global analysis of saliva as a source of bacterial genes for insights into human population structure and migration studies – Karsten Henne – BMC Evolutionary Biology

“By focussing on the house-keeping gene gdh .., on the virulence gene gtf .. of mitis-streptococci and on the 16S-23S rRNA internal transcribed spacer (ITS) region of the Fusobacterium nucleatum/periodonticum-group we here tested the hypothesis that bacterial genes from human saliva have the potential for distinguishing human populations.’

Microbial community in persistent apical periodontitis: a 16S rRNA gene clone library analysis – M. N. Zakaria – International Endodontic Journal

“Whilst a diverse bacterial species were observed in the persistent apical lesions, some characteristic patterns of bacterial community were found in the symptomatic lesions. “

The Adenoid Microbiome in Recurrent Acute Otitis Media and Obstructive Sleep Apnea – Carolyn P. Ojano-Dirain – Otolaryngology – Head and Neck Surgery

“Microbes are present on all adenoid specimens, however, the microbial profile differs between recurrent AOM and OSA.”

Human gut microbiome

Susceptibility to Campylobacter Infection Is Associated with the Species Composition of the Human Fecal Microbiota – Johan Dicksved – mBio

“Here we address this by prospectively studying the gut microbiota composition before, during, and after natural Campylobacter infection in exposed poultry abattoir workers.”

Eukaryote Culturomics of the Gut Reveals New Species – Nina Gouba, Didier Raoult, Michel Drancourt – PLOS ONE

“We further explored this repertoire using PCR-sequencing and culture in seven individuals living in four tropical countries. A total of 41 microeukaryotes including 38 different fungal species and three protists were detected. “

Review: Decade in review—gut microbiota: The gut microbiota era marches on – Francisco Guarner – Nature Reviews Gastroenterology & Hepatology

“Research on the gut microbial communities harboured in the human gut is progressing rapidly owing to the availability of novel and reliable tools for analysis.”

Modulation of Fecal Clostridiales Bacteria and Butyrate by Probiotic Intervention with Lactobacillus paracasei DG Varies among Healthy Adults – Chiara Ferrario – Journal of Nutrition

“High-throughput 16S ribosomal RNA gene sequencing was used to characterize the fecal microbiota in healthy adults (23–55 y old) of both sexes, before and after 4 wk of daily consumption of a capsule containing at least 24 billion viable Lactobacillus paracasei DG cells”

Review: The gut microbiota, bacterial metabolites and colorectal cancer – Petra Louis, Georgina L. Hold & Harry J. Flint – Nature Reviews Microbiology

“In this Review, we discuss the relationship between diet, microbial metabolism and CRC and argue that the cumulative effects of microbial metabolites should be considered in order to better predict and prevent cancer progression.”

Changes of the human gut microbiome induced by a fermented milk product – Patrick Veiga – Nature Scientific Reports

“Our data challenge the view that microbes ingested with food have little impact on the human GM functioning and rather provide support for beneficial health effects.”

Gut Microbiome and Multiple Sclerosis – Pavan Bhargava, Ellen M. Mowry – Current Neurology and Neuroscience Reports

“We examine the different sources of information linking the gut microbiota to multiple sclerosis and examine the future avenues for utilizing the knowledge of the gut microbiome to potentially treat and prevent multiple sclerosis.”

Microbial Modulation of Insulin Sensitivity – Muhammad Tanweer Khan, Max Nieuwdorp, Fredrik Bäckhed – Cell Metabolism

“The gut microbiota has emerged as an integral factor that impacts host metabolism and has been suggested to play a vital role in metabolic diseases such as obesity, insulin resistance, type 2 diabetes, and cardiovascular disease.”

Gut Microbial Community Structure and Complications After Kidney Transplantation: A Pilot Study – Lee, John R – Transplantation

“We characterized bacterial composition by polymerase chain reaction amplification of the 16S rRNA V4-V5 variable region and deep sequencing using the Illumina MiSeq platform.’

Human genital microbiome

Association between cigarette smoking and the vaginal microbiota: a pilot study – Rebecca M Brotman – BMC Infectious Diseases

“Smokers had a lower proportion of vaginal Lactobacillus spp. compared to non-smokers.”

Pregnancy and birth

Human Breast Milk – The Magic In The Microbiome – Science20

“Ma et al (2014 submitted manuscript) recently postulated that the opportunistic pathogen such as Staphylococcus aureus, which has been confirmed to exist in the human milk microbiome, is normally suppressed by a network of beneficial bacteria coexisted in the breast milk microbiome, but may become source of infectious mastitis when the host environment permits.”

Animal models of human microbiome research

Antibiotic Treatment of Pregnant Non-Obese Diabetic Mice Leads to Altered Gut Microbiota and Intestinal Immunological Changes in the Offspring – N. Tormo-Badia – Scandinavian Journal of Immunology

“we found a differential clustering of gut microbiota in the offspring from NOD mothers treated with antibiotics during gestation compared with offspring from control mothers.”

Shifts in microbiota species and fermentation products in a dietary model enriched in fat and sucrose – U. Etxeberria – Beneficial Microbes

“The aim of the present study was to identify gut microbiota dysbiosis and associated metabolic changes produced in male Wistar rats fed a HFS diet for 6 weeks and compare it with the basal microbial composition.”

The short chain fatty acids, butyrate and propionate, have differential effects on the motility of the guinea pig colon – Norm R. Hurst – Neurogastroenterology & Motility

“We hypothesized that the effect of SCFAs on colonic motility varies with chain length and aimed to determine the effects of SCFAs on propagating and non-propagating contractions of guinea pig proximal and distal colon.”

Small Bowel Resection Induces Long-Term Changes in the Enteric Microbiota of Mice – J. Sommovilla – Journal of Gastrointestinal Surgery

“Bowel resection induces long-term changes in the microbial community of the murine ileum, but not at more distal sites of the gastrointestinal tract. “

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Human microbiome digest, September 15, 2014

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MicrobiomeDigest is back! Lots of new papers came out in my 2-week hiatus, so here we go (more tomorrow):

General (Human) Microbiota

Editorial for Special Issue: Insights into Molecular Mechanisms of Microbiota – Eric C. Martens, Justin L. Sonnenburg, David A. Relman – Journal of Molecular Biology

“Understanding the molecular mechanisms that underlie these processes has been a goal for decades, but while recent technological advances have greatly expanded our descriptive view of these ecosystems, our knowledge of underlying functions and mechanisms has lagged. “

A Systematic Analysis of Biosynthetic Gene Clusters in the Human Microbiome Reveals a Common Family of Antibiotics – Mohamed S. Donia – Cell

“we identified 3,118 small-molecule biosynthetic gene clusters (BGCs) in genomes of human-associated bacteria and studied their representation in 752 metagenomic samples from the NIH Human Microbiome Project.”

See also:

Mining for Antibiotics, Right Under Our Noses – Carl Zimmer – New York Times

The Integrative Human Microbiome Project: Dynamic Analysis of Microbiome-Host Omics Profiles during Periods of Human Health and Disease – iHMP Consortium – Cell Host & Microbe

“Here we describe the three models of microbiome-associated human conditions, on the dynamics of preterm birth, inflammatory bowel disease, and type 2 diabetes”

Microbiome in pregnancy and birth
Review: Diet and host–microbial crosstalk in postnatal intestinal immune homeostasis – Nitya Jain & W. Allan Walker – Nature Reviews Gastroenterology & Hepatology

“In this Review, we discuss the current state of knowledge regarding early-life nutrition, its effects on the microbiota and the consequences of diet-induced perturbation of the structure of the microbial community on mucosal immunity and disease susceptibility.”

The early use of appropriate prophylactic antibiotics in susceptible women for the prevention of preterm birth of infectious etiology – Jan Stener Joergensen – Expert Opinion on Pharmacotherapy

“a focused systematic review/meta-analysis, which targeted the use of clindamycin before 22 weeks gestation, in women with objective evidence of abnormal genital tract flora, demonstrated that clindamycin produced a significant decrease in late miscarriage and preterm birth.”

Mucosa-Associated Bacterial Diversity in Necrotizing Enterocolitis – Rachel Brower-Sinning – PLOS ONE

“26 intestinal samples were resected from 19 infants, including 16 NEC samples and 10 non-NEC samples. Bacterial 16S rRNA gene sequences were amplified and sequenced. “

Oral human microbiome

The presence of cariogenic and periodontal pathogens in the oral cavity of one-year-old
infants delivered pre-term with very low birthweights: a case control study – Vlasta Merglova – BMC Oral Health

“At 12 months of age, both groups of infants were examined, and unstimulated saliva samples from the dorsum of the tongue and dental plaque samples were collected.”

Frequent detection of Streptococcus tigurinus in the human oral microbial flora by a specific 16S rRNA gene real-time TaqMan PCR – Andrea Zbinden – BMC Microbiology

“Although S. tigurinus was a frequently detected species of the human oral microbial flora, it was not associated with periodontal disease. “

Oral Microbiome Link to Neurodegeneration in Glaucoma – Konstantin Astafurov – PLOS ONE

“Mouthwash specimens from patients with glaucoma and control subjects were analyzed for the amount of bacteria”

Bacterial community composition of chronic periodontitis and novel oral sampling sites for detecting disease indicators  – Vaia Galimanas – Microbiome

“Using SubG, SupG, and tongue plaque DNA from 11 healthy and 13 diseased subjects, we sequenced V3 regions (approximately 200 bases) of the 16S rRNA gene using Illumina sequencing.”

Human gut microbiome

TLR5-Mediated Sensing of Gut Microbiota Is Necessary for Antibody Responses to Seasonal Influenza Vaccination – Jason Z. Oh – Immunity

“TLR5-mediated sensing of the microbiota also impacted antibody responses to the inactivated polio vaccine, but not to adjuvanted vaccines or the live-attenuated yellow fever vaccine.”

Review: Nutritional iron turned inside out: intestinal stress from a gut microbial
perspective – Guus A.M. Kortman – FEMS Microbiology Reviews

“This review covers the multifaceted aspects of nutritional iron stress with respect to growth, composition, metabolism and pathogenicity of the gut microbiota in relation to human health.”

Review: Host–microbe interactions shaping the gastrointestinal environment – Gerard E. Kaiko, Thaddeus S. Stappenbeck – Trends in Immunology

“Here we review emerging concepts of how microbial metabolic processes control commensal composition, invading pathogens, immune activation, and intestinal barrier function. “

The microbial eukaryote Blastocystis is a prevalent and diverse member of the healthy human gut microbiota – Pauline D. Scanlan – FEMS Microbiology Ecology

“Here, we survey the prevalence, genetic diversity and temporal stability of Blastocystis in a group of healthy adults (n = 105) using a sensitive PCR assay.”

Evaluation of bifidobacterial community composition in the human gut by means of a targeted amplicon sequencing (ITS) protocol – Christian Milani – FEMS Microbiology Ecology

“Here, we define the internal transcribed spacer (ITS) sequences of all currently known Bifidobacterium taxa, providing a Bifidobacterium-specific primer pair that targets a hypervariable region within the ITS suitable for precise taxonomic identification of all 48 so far recognized members of the Bifidobacterium genus.”

Alzheimer’s disease and the microbiome – James M. Hill – Alzheimer’s & Dementia

“In these preliminary studies we evaluated the effects of the anti-amyloid, anti-oxidant, anti-inflammatory flavonoid quercetin on growth inhibition of the HM-representative Bacteroides galacturonicus (ATCC 43244).”

Complete Suppression of the Gut Microbiome Prevents Acute Graft-Versus-Host Disease following Allogeneic Bone Marrow Transplantation  – Jaak M. Vossen – PLOS ONE

“All patients received T-cell replete marrow from human leukocyte antigens (HLA) matched sibling donors under identical transplantation conditions.”

Associations of the Fecal Microbiome With Urinary Estrogens and Estrogen Metabolites in Postmenopausal Women – Barbara J. Fuhrman – Journal of Clinical Endocrinology & Metabolism

“Our data suggest that women with a more diverse gut microbiome exhibit an elevated urinary ratio of hydroxylated estrogen metabolites to parent estrogen. “

Alterations of the human gut microbiome in liver cirrhosis – Nan Qin – Nature

“Here we characterize the gut microbiome in liver cirrhosis by comparing 98 patients and 83 healthy control individuals. “

Altered intestinal microbiota and blood T cell phenotype are shared by patients with Crohn’s disease and their unaffected siblings – Charlotte R Hedin – Gut

“Faecal microbiology was analysed by quantitative PCR targeting 16S ribosomal RNA, FC by ELISA, blood T cell phenotype by flow cytometry and IP by differential lactulose-rhamnose absorption in 22 patients with inactive CD, 21 of their healthy siblings and 25 controls.”

Detection of bacterial DNA in lymph nodes of Crohn’s disease patients using high throughput sequencing – Claire L O’Brien – Gut

“Universal primers targeting V1–V3 regions of bacterial 16S rRNA genes were used to amplify bacterial DNA and amplicons sequenced using high throughput sequencing. “

Cultivation-based multiplex phenotyping of human gut microbiota allows targeted recovery of previously uncultured bacteria – Elizabeth A. Rettedal – Nature Communications

“Here, we show that carefully designed conditions enable cultivation of a representative proportion of human gut bacteria, enabling rapid multiplex phenotypic profiling. “

Animal models of human microbiome research

Innate lymphoid cells regulate intestinal epithelial cell glycosylation – Yoshiyuki Goto – Science

“Here, we show that type 3 innate lymphoid cells (ILC3) induced intestinal epithelial Fut2 expression and fucosylation in mice. “

Effect of Metformin on Metabolic Improvement and Gut Microbiota – Heetae Lee and GwangPyo Ko – Applied and Environmental Microbiology

“In this study, the composition of the gut microbiota was investigated using a mouse model of high-fat-diet (HFD)-induced obesity with and without metformin treatment. “

Microbiota modulate transcription in the intestinal epithelium without remodeling the accessible chromatin landscape – J. Gray Camp – Genome Research

“We profiled transcriptome and accessible chromatin landscapes in intestinal epithelial cells (IECs) from mice reared in the presence or absence of microbiota.”

Host adaptive immunity alters gut microbiota – Husen Zhang – ISME Journal

“Here we investigated the role of adaptive immunity on the mouse distal gut microbial composition by sequencing 16 S rRNA genes from microbiota of immunodeficient Rag1−/− mice, versus wild-type mice, under the same housing environment.”

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Microbiome Digest, August 29, 2014

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@MicrobiomDigest will be enjoying vacation for the next two weeks, so I won’t be able to post as much as usual. I might occasionally have some time and internet access at the same time, and post something, but don’t rely on this blog during that time for your daily Microbiome fix. But I will be back! Enjoy this last (short) one for now:
Human oral microbiome

Bacterial community composition of chronic periodontitis and novel oral sampling sites for detecting disease indicators – Vaia Galimanas – Microbiome

Human gut microbiome

Immunoglobulin A Coating Identifies Colitogenic Bacteria in Inflammatory Bowel Disease – Noah W Palm – Cell

Modulation of immune development and function by intestinal microbiota – Agnieszka M. Kabat – Trends in Immunology

 

Worms, bacteria, and micronutrients: an elegant model of our diet – Lutfu Safak Yilmaz, Albertha J.M. Walhout – Trends in Genetics

 

Mammal microbiome

Spatial heterogeneity of gut microbiota reveals multiple bacterial communities with distinct characteristics (in flying squirrels) – Hsiao-Pei Lu – Scientific Reports

Social influences on the gut microbiome of developing monkeys – W.Z. Amaral – Brain, Behavior, and Immunity

 

Do Rumen Bacteroidetes Utilize an Alternative Mechanism for Cellulose Degradation? – AE Naas – mBio

 

Characterization of the Fecal Microbiota of Pigs before and after Inoculation with “Brachyspira hampsonii” – Matheus O. Costa – PLOS ONE

 

Sponges and corals

The versatile nature of coral-associated viruses – Bettarel Yvan – Environmental Microbiology

Onset and establishment of diazotrophs and other bacterial associates in the early life history stages of the coral Acropora millepora – Kimberley A. Lema – Molecular Ecology

Rocks and Water Microbiome

Microbial Colonization of Bare Rocks: Laboratory Biofilm Enhances Mineral Weathering – F. Seiffert – Procedia Earth and Planetary Science

Microbial diversity and biogeochemical cycling in soda lakes – Dimitry Y. Sorokin – Extremophiles

Food microbiome

Switzerland Puts Secret Bacteria In Cheese To Catch Knockoffs – Sarah Zhang – Gizmodo

Bioinformatics

A Scalable and Accurate Targeted Gene Assembly Tool (SAT-Assembler) for Next-Generation Sequencing Data – Yuan Zhang – PLOS Computational Biology

Metabolomics

Taking your breath away: metabolomics breathes life in to personalized medicine
Nicholas J.W. Rattray – Trends in Biotechnology

Phages and Viruses

Identifying and analyzing bacteriophages in human fecal samples: what could we discover? – Maite Muniesa1 & Juan Jofre – Future Medicine

Microbes in the news

Hotel rooms aren’t yucky – you colonize them with your own personal bacteria within hours — Rachel Feltman – Washington Post

A touching story: The ancient conversation between plants, fungi and bacteria – David Tenenbaum – News UW Madison

Bik’s Picks

The universal ‘anger face’: Each element makes you look physically stronger and more formidable – Science Daily

Zombie Bacteria Invasion? Nothing To Worry About – Science 2.0

Report: Ice Bucket Challenge Causing Ecological Mayhem in California – The Allium (Satire)

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Human microbiome, August 26, 2014

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Gut microbiome structure in the first years of life, lung microbiome in pneumonia and tuberculosis, why iron supplements might not always be a good thing, and the Microbiome Diet Book.

Pregnancy and birth

* The Intestinal Microbiome in Early Life: Health and Disease – Marie-Claire Arrieta – Frontiers in Immunology

“This review describes the gut microbiome structure and function during the formative first years of life, as well as the environmental factors that determine its composition.”

Oral microbiome

Review: The oral microbiome diversity and its relation to human diseases – Jinzhi He – Folia Microbiologica

“In this review, we focus on the recent progress in this field, including the oral microbiome composition and its association with human diseases.”

Respiratory microbiome

Single-Molecule Long Read 16S Sequencing to Characterize the Lung Microbiome from Mechanically Ventilated Patients with Suspected Pneumonia – Ian Toma – Journal of Clinical Microbiology

“The present study used NGS of essentially full-length PCR-amplified 16S ribosomal DNA from the bronchial aspirates of intubated patients with suspected pneumonia.”

* Respiratory tract clinical sample selection for microbiota analysis in patients with pulmonary tuberculosis – Luz Elena Botero – Microbiome Journal

“Most V1-V2 16S rRNA gene sequences belonged to the phyla Firmicutes, Bacteroidetes, Proteobacteria, Actinobacteria, and Fusobacteria, with differences in relative abundances and in specific taxa associated with each sample type. “

Gut microbiome

* Iron fortification adversely affects the gut microbiome, increases pathogen abundance and induces intestinal inflammation in Kenyan infants – Tanja Jaeggi – Gut

“Using pyrosequencing, +FeMNPs increased enterobacteria, particularly Escherichia/Shigella (p=0.048), the enterobacteria/bifidobacteria ratio (p=0.020), and Clostridium (p=0.030).”

Animal models of microbiome research

Amelioration of DSS-induced murine colitis by VSL#3 supplementation is primarily associated with changes in ileal microbiota composition – Jordan S. Mar – Gut Microbes

“Microbiota profiling revealed distinct bacterial community compositions in the ileum, cecum and colon of control untreated animals”

Commensal Bacteria Regulate Thymic Aire Expression – Akihito Nakajima – PLOS ONE

“autoimmune regulator (Aire) expression in thymic epithelial cells (TECs), main components of the thymic microenvironment, was decreased in comparison to specific pathogen-free (SPF) mice and Nod1 wild-type (WT) mice, respectively. “

Microbiome in the News

* Overselling the Microbiome Award: The Microbiome Diet Book – Jonathan Eisen – The Tree of Life

“Sound too good to be true? Well, that is because it is.”

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