Category Archives: Pregnancy and birth

Microbiome digest, September 23, 2014

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I don’t have much time tonight, so I’ll keep it short.

Pregnancy and birth

Homogeneity of the Vaginal Microbiome at the Cervix, Posterior Fornix, and Vaginal Canal in Pregnant Chinese Women – Yi-E Huang- Microbial Ecology

Impact of Feeding and Medical Practices on the Development of Necrotizing Enterocolitis – Brian L. Montenegro, Camilia R. Martin – Current Pediatrics Reports

Human respiratory microbiome

Expanding Our Understanding of Respiratory Microbiota in Cystic Fibrosis – John J. LiPuma – Annals of the American Thoracic Society

Microbiota in the throat and risk factors of laryngeal carcinoma – Hongli Gong – Applied and Environmental Microbiology

Human gut microbiome

Membership and Behavior of Ultra-Low-Diversity Pathogen Communities Present in the Gut of Humans during Prolonged Critical Illness – Alexander Zaborin – mBio

The Overarching Influence of the Gut Microbiome on End-Organ Function: The Role of Live Probiotic Cultures – Luis Vitetta – Pharmaceuticals

Excretion of host DNA in feces is associated with risk of Clostridium difficile infection –  Caroline Vincent – Journal of Immunology Research

Animal and in vitro studies of human microbiome

Effect of Oral Administration of Metronidazole or Prednisolone on Fecal Microbiota in Dogs – Hirotaka Igarashi – PLOS ONE

Age and Microenvironment Outweigh Genetic Influence on the Zucker Rat Microbiome
Hannah Lees – PLOS ONE

A comparative evaluation of prebiotic oligosaccharides using in vitro cultures of infant fecal microbiome – J Stiverson – Applied and Environmental Microbiology

Alterations in Ileal Mucosa Bacteria Related to Diet Complexity and Growth Performance in Young Pigs – Crystal L. Levesque – PLOS ONE

Mammal microbiome

Fecal microbial diversity and putative function in captive western lowland gorillas (Gorilla gorilla gorilla), common chimpanzees (Pan troglodytes), Hamadryas baboons (Papio hamadryas), and binturongs (Arctictis binturong) – Erin A. McKenney – Integrative Zoology

Pathogenic Eukaryotes in Gut Microbiota of Western Lowland Gorillas as Revealed by Molecular Survey – Ibrahim Hamad – Scientific Reports

Insect microbiome

Routes of acquisition of the gut microbiota of Apis mellifera – J. Elijah Powell – Applied and Environmental Microbiology

Sponge microbiome

Symbiotic archaea in marine sponges show stability and host specificity in community structure and ammonia oxidation functionality – Fan Zhang – FEMS Microbiology Ecology
http://onlinelibrary.wiley.com/doi/10.1111/1574-6941.12427/abstract

Plant microbiome

Comparison of root system architecture and rhizosphere microbial communities of Balsas teosinte and domesticated corn cultivars – Márton Szoboszlay – Soil Biology and Biochemistry

Micromonospora from nitrogen fixing nodules of alfalfa (Medicago sativa L.). A new promising Plant Probiotic Bacteria – Pilar Martínez-Hidalgo – Scientific Reports

Effects of Clonal Integration on Microbial Community Composition and Processes in the Rhizosphere of the Stoloniferous Herb Glechoma longituba (Nakai) Kuprian – Ningfei Lei – PLOS ONE

Soil type dependent effects of a potential biocontrol inoculant on indigenous bacterial communities in the rhizosphere of field-grown lettuce – Susanne Schreiter – FEMS Microbiology Ecology

Soil microbiome

Culturable fungal assemblages growing within Cenococcum sclerotia in forest soils – Keisuke Obase – FEMS Microbiology Ecology

Food microbiology

Dynamic changes of the microbial communities during the preparation of traditional Tibetan Qula cheese – Bei Zhang – Dairy Science & Technology

Metabolomics / Functional metagenomics

Identification of Aminoglycoside and β-Lactam Resistance Genes from within an Infant Gut Functional Metagenomic Library – Fiona Fouhy – PLOS ONE

Mining the Metabiome: Identifying Novel Natural Products from Microbial Communities

Aleksandr Milshteyn, Jessica S. Schneider, Sean F. Brady – Chemistry & Biology

Commensally sourced antibiotics – Cláudio Nunes-Alves – Nature Reviews Microbiology

Impact of dietary polydextrose fiber on the human gut metabolome – Santosh Lamichhane – Journal of Agricultural and Food Chemistry

Preserving the earth’s microbes for drug discovery in the future – Ranjith N. Kumavath and Satyanarayana S.V – Journal of Microbiology and Microbial Research

Microbial Ecology

PNAS has a special issue this week on Biogeography (with the Panama forest trees paper by Jessica Green): The emergence and promise of functional biogeography – Cyrille Violle – PNAS

Active invasion of bacteria into living fungal cells – Nadine Moebius – eLife

Microbes in the news

Microbiome: You are never alone – John A Goldman – Atlanta Medicine

Seeking the Sweet Spot, from Mouth to Microbiome – David Katz – Huffington Post

New evidence suggests long-term relationships with bacteria begins before we’re born – Norbert Berzog and David Niesel – Galveston County Daily News

MIT Developing Ship-Repairing Bacteria – World Maritime News

Science and publishing

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

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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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Microbiome digest, September 18, 2014

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It’s an exciting day at MicrobiomeDigest, with an Ig Nobel Prize awarded to the baby poop sausages paper, the Breaking Bad of gut microbiota, the microbiome of salami, and how bacteria can help in agriculture. Here we go:

Respiratory microbiome

Persistence of livestock-associated antibiotic-resistant Staphylococcus aureus among industrial hog operation workers in North Carolina over 14 days – Maya Nadimpalli – Occupational & Environmental Medicine (see also below)

“Nasal carriage of livestock-associated S. aureus, multidrug-resistant S. aureus and methicillin-resistant S. aureus can persist among industrial hog operation workers over a 14-day period, which included up to 96 h away from work.”

Human gut microbiome

Breaking Bad – the two sides of gut microbiota in portal hypertension – Gautam Mehta and Rajeshwar P Mookerjee – Liver International

“In this issue of Liver International, Rincon and colleagues bring these threads together by exploring the effects of modulating gut flora on portal hypertension in the context of decompensated cirrhosis.”

Pregnancy and birth

Winners of the 2014 Ig Nobel Prize in Nutrition – ABC News

2014 IgNobel Prize in Nutrition: “Raquel Rubio, Anna Jofra, Belen Martin, Teresa Aymerich and Margarita Garriga, for their study of using infant fecal bacteria as potential probiotic starter cultures for fermented sausages.”

Plant microbiome

Why Tiny Microbes Mean Big Things for Farming – Peter Andrey Smith – National Geographic

“The soil-dwelling bacteria that we walk on every day are working their way into technologies that could help feed the world.”

Plant interactions with other organisms: molecules, ecology and evolution – Amy T. Austin and Carlos L. Ballaré – New Phytologist

“There are still many open questions regarding how plant interactions with other organisms are shaped by evolutionary forces over time. “

Food microbiology

Bacterial diversity in typical Italian salami at different ripening stages as revealed by high-throughput sequencing of 16S rRNA amplicons – Justyna Połka – Food Microbiology

“Salame Piacentino PDO was analysed by HTS (Illumina) of 16S rRNA amplicons.”

Techniques

1-day bowel preparation with polyethylene glycol 3350 is as effective and safe as a 3-day preparation for colonoscopy in children – Serge A Sorser – BMC Research Notes

“There were no differences between the groups in efficacy of bowel preparation based on colonoscopic grading or the safety of the preparation.”

Viruses and phages

Metagenomic Analysis of Double-stranded DNA viruses in Healthy Adults – Kristine M. Wylie – BMC Biology

“We analyzed eukaryotic double-stranded DNA (dsDNA) viruses, together with dsDNA replicative intermediates of single-stranded DNA viruses, in metagenomic sequence data generated by the HMP. “

see also: Your own personal virome – Biome – BioMedCentral

“If life gives you lemons, you make lemonade. And if your bacterial DNA datasets give you viral DNA contaminants, you use them to study the virome. “

Bioinformatics

Estimating overannotation across prokaryotic genomes using BLAST+, UBLAST, LAST and BLAT – Gabriel Moreno-Hagelsieb and Brigitte Hudy-Yuffa – BMC Research Notes

“Despite faster programs miss sequence matches otherwise found by NCBI?s BLAST, the overannotation estimates are very similar and thus these programs can be used with confidence for this task.”

Antibiotic and resistance

Single-molecule sequencing to track plasmid diversity of hospital-associated carbapenemase-producing Enterobacteriaceae – Sean Conlan – Science Translational Medicine

“we performed comprehensive surveillance and genomic sequencing of carbapenem-resistant Enterobacteriaceae in the National Institutes of Health (NIH) Clinical Center patient population and hospital environment. “

U.S. Lays Out Strategy to Combat Crisis of Antibiotic Resistance – Sabrina Tavernise – NY Times

“The Obama administration on Thursday announced measures to tackle the growing threat of antibiotic resistance”

Factory-Farm Workers Found to Carry High Levels of Antibiotic-Resistant Bacteria – Willy Blackmore – TakePart (see also above)

“While only one worker was found to be carrying MRSA after nostril swabs were tested, 86 percent carried staph bacteria associated with livestock—far higher than the general population. “

Microbes in the News

Microbirth: The Extra Question Every Expectant Mother Needs To Ask – Toni Harman – Huffington Post

“The doctor or midwife looks at the expectant mother blankly. “I’m sorry. I have never heard of the microbiome. And I’ve never heard of Microbirth.”

Science, publishing, and career

Rhubarb pie and science – Sandy Becker – Science Working Life

“When I am asked how I became a developmental biologist, I say, “Jim hired me for my rhubarb pie and my Phi Beta Kappa key, and the rest is history.””

Can Post-Publication Peer-Reviews Increase Research Transparency? – Liz Allen – Berkeley Bitts

“When Peer Review is done in the open by named individuals, we believe it should be more constructive and issues will surface more quickly.”

 

Bik’s Picks

Winners of the 2014 Ig Nobel Awards – ABC News

“The 2014 Ig Nobel winners, awarded Thursday at Harvard University by the Annals of Improbable Research magazine”

Europeans drawn from three ancient ‘tribes’ – Paul Rincon – BBC News

“The modern European gene pool was formed when three ancient populations mixed within the last 7,000 years, Nature journal reports.”

Bowl Half Empty: Dogs Can Be Pessimists – Richard Farrell – Discovery

“New PhD research out of the University of Sydney by Dr. Melissa Starling, from the school’s Faculty of Veterinary Science, sought to find out if dogs had underlying personalities that tended toward either optimism of pessimism.”

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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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Microbiome digest, August 27, 2014

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Not many microbiome papers today, just some other interesting topics: does dirt make you happy, definition of preterm labor, cheese cultures, and solving a Death Valley mystery.

Pregnancy and birth 

The Problem With What Doctors Call Preterm Labor – Catherine Pearson – Huffington Post

“”We have been thinking of preterm birth as though it is one condition, and this is not the right way of thinking about the problem,” Dr. Roberto Romero, chief of the perinatology research branch of the Eunice Kennedy Shriver National Institute of Child Health and Human Development, told The Huffington Post.”

Insect microbiome

* Identifying the core microbial community in the gut of fungus-growing termites – Saria Otani – Molecular Ecology

“Using 454-pyrosequencing of the 16S rRNA gene, we show that gut communities have representatives of 26 bacterial phyla and are dominated by Firmicutes, Bacteroidetes, Spirochaetes, Proteobacteria and Synergistetes”

Microbes in the news

* Does Dirt Make You Happy? – Anna Brones – Modern Farmer

“We benefit from being outdoors and exposed to things like soil and animals, because of the fact that we’re exposed to microorganisms.”

* Scientists and cheesemakers gather for (microbial) culture – Ewen Callaway – Nature News

““I fall in love every time I look at a cheese rind. They’re wonderful microbial ecosystems,” she says.”

Transcriptomics

Comparative analysis of the transcriptome across distant species – Mark B. Gerstein – Nature

“To this end, the ENCODE and modENCODE consortia have generated large amounts of matched RNA-sequencing data for human, worm and fly. “

Bik’s Picks

This has intrigued me for years – very happy to see this paper.
Sliding Rocks on Racetrack Playa, Death Valley National Park: First Observation of Rocks in Motion – Richard D. Norris – PLOS ONE

“the process of rock movement that we have observed occurs when the thin, 3 to 6 mm, “windowpane” ice sheet covering the playa pool begins to melt in late morning sun and breaks up under light winds of ~4–5 m/s.”

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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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Human microbiome digest, August 25, 2014

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Oral microbiome in the settings of periodontitis, smoking and antibiotic resistance, respiratory microbiome in Cystic Fibrosis, a decade of molecular papers on vaginal microbiome, and gut bacteria protecting against food allergies.

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 analyzed for the presence of >250 species/phylotypes using HOMIM. “

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.”

Extended-spectrum beta-lactamase-producing bacteria are not detected in supragingival plaque samples from human fecal carriers of ESBL-producing Enterobacteriaceae – Arne Søraas – Journal of Oral Microbiology

“No ESBL-producing bacteria or ESBL genes were detected using culture-based and molecular methods. “

Clonality of bacterial consortia in root canals and subjacent gingival crevices – Nipuna B. Parahitiyawa – Journal of Investigative and Clinical Dentistry

“The four niches studied yielded 186 clones representing 54 phylotypes. Clone library comparisons using LIBSHUFF software indicated that each niche was inhabited by a unique flora. “

Respiratory microbiome

* Antimicrobial resistance in the respiratory microbiota of people with cystic fibrosis –
Laura J Sherrard – The Lancet

“Strategies to manage antimicrobial resistance consist of new antibiotics or localised delivery of antimicrobial agents, iron sequestration, inhibition of quorum-sensing, and resistome analysis.”

Evidence that Intraspecific Trait Variation among Nasal Bacteria Shapes the Distribution of Staphylococcus aureus – Ben Libberton – Infection and Immunity

“We characterized S. aureus growth inhibition by the culturable bacterial aerobe consortia of 60 nasal microbiomes, and this revealed intraspecific variation in growth inhibition and that inhibitory isolates clustered within communities that were culture negative for S. aureus. “

Gary Huffnagle: rewriting the rules on the lung microbiome – David Holmes – The Lancet

“The ideas being generated by Huffnagle at the moment are all about the lung microbiome and its role in the pathogenesis of everything from chronic obstructive pulmonary disease (COPD) to asthma, and they’re starting to make waves.”

Vaginal microbiome

* The Vaginal Microbiota: What Have We Learned after a Decade of Molecular Characterization? – Janneke H. H. M. van de Wijgert – PLOS ONE

“We conducted a systematic review of the Medline database … to determine if consistent molecular vaginal microbiota (VMB) composition patterns can be discerned after a decade of molecular testing, and to evaluate demographic, behavioral and clinical determinants of VMB compositions.”

Gut microbiome

Modelling the Emergent Dynamics and Major Metabolites of the Human Colonic Microbiota – Helen Kettle – Environmental Microbiology

“We present here a first attempt at modelling microbial dynamics in the human colon incorporating both uncertainty and adaptation. “

Animal models of human microbiome

Commensal bacteria protect against food allergen sensitization – Andrew T. Stefka – PNAS USA

“By selectively colonizing gnotobiotic mice, we demonstrate that the allergy-protective capacity is conferred by a Clostridia-containing microbiota. “

Pregnancy and Birth

Researcher Granted $1 Million to Study Deadly Bacteria Passed to Babies From 25 Percent of Mothers – Infection Control Today

“Narayana Sthanam, PhD, professor of structural biology in the Department of Optometry, has been awarded a four-year, $1 million R01 grant from the National Institute of Allergy and Infectious Diseases, part of the National Institutes of Health, to further Group B Streptococcus research.”

Microbiome News

* Satire: Study Reveals Microbiome To Be Master-Controller Of All Humanity – The Allium

“Science has already found out that your microbiome at birth decides your taste in clothes and music, whether you are going to be great footballer like David Beckham or a great political leader like Sarah Palin.”

9 questions you were too grossed out to ask about the bacteria living on you – Susannah Locke – Vox

“What researchers have discovered is that our bodies are essentially complex ecosystems of tiny living things. “

Interview with Prof. Yolanda Sanz, project coordinator of My New Gut – Kristina Campbell – Gut Microbiota For Health

“Professor Yolanda Sanz has been appointed MyNewGut’s project coordinator and leads the project’s human intervention trials on the gut microbiome’s ability to metaolise (sic) nutrients and influence energy balance. “

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