Author Archives: eliesbik

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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Microbiome digest, September 17, 2014

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Human gut microbiome and artificial sweeteners, cholera recovery, or ancient coprolites, protbiotics and the brain, coastal soil, diversity and science, metabolomics, and Bik’s Picks.
Human gut microbiome

Artificial sweeteners induce glucose intolerance by altering the gut microbiota – Jotham Suez – Nature

“We identify NAS-altered microbial metabolic pathways that are linked to host susceptibility to metabolic disease, and demonstrate similar NAS-induced dysbiosis and glucose intolerance in healthy human subjects.”

Members of the human gut microbiota involved in recovery from Vibrio cholerae infection – Ansel Hsiao – Nature

“We find that recovery is characterized by a pattern of accumulation of bacterial taxa that shows similarities to the pattern of assembly/maturation of the gut microbiota in healthy Bangladeshi children”

Paleomicrobiology: Revealing Fecal Microbiomes of Ancient Indigenous Cultures – Raul J. Cano – PLOS ONE

“We analyzed human coprolites from the Huecoid and Saladoid cultures from a settlement on Vieques Island, Puerto Rico.”

Animal models of microbiome research

Modulation of Intestinal Microbiota by the Probiotic VSL#3 Resets Brain Gene Expression and Ameliorates the Age-Related Deficit in LTP – Eleonora Distrutti – PLOS ONE

“Here, we report that treatment of aged rats with VSL#3 induced a robust change in the composition of intestinal microbiota with an increase in the abundance of Actinobacteria and Bacterioidetes, which was reduced in control-treated aged rats.”

Soil microbiome

Unravelling the Carbon and Sulphur Metabolism in Coastal Soil Ecosystems Using Comparative Cultivation-Independent Genome-Level Characterisation of Microbial Communities – Basit Yousuf – PLOS ONE

“Distinct compositional differences were observed among the clone libraries, which revealed a dominance of phylotypes associated with carbon and sulphur cycling”

Techniques

Partition Enrichment of Nucleotide Sequences (PINS) – A Generally Applicable, Sequence Based Method for Enrichment of Complex DNA Samples – Thomas Kvist, Line Sondt-Marcussen, Marie Just Mikkelsen – PLOS ONE

“The present paper describes a new method, Probability directed Isolation of Nucleic acid Sequences (PINS), for enrichment of DNA, enabling the sequencing of a large DNA region surrounding a small known sequence. “

Metabolomics

Of Monkeys and Men: A Metabolomic Analysis of Static and Dynamic Urinary Metabolic Phenotypes in Two Species – Edoardo Saccenti – PLOS ONE

“we show that despite the standardization of diet as the most relevant extrinsic factor, a clear individual and discriminative metabolic fingerprint also exists for monkeys.”

Science and Career

Diversity: Pride in science – M Mitchell Waldrop – Nature

“The sciences can be a sanctuary for gay, lesbian, bisexual and transgender individuals, but biases may still discourage many from coming out.”

Bik’s Picks

Only 4 of them are women…. – The top 50 science stars of Twitter – Jia You – Science

“Though Hall says he meant his K-index lightheartedly, his article in Genome Biology sparked a Twitter storm of criticism. So just who are the Kardashians of science, and is Hall’s criticism justified?”

Breast milk reveals a correlation between dietary fats and academic success – Science Daily

“You are what you eat, the saying goes, and now a study conducted by researchers at UC Santa Barbara and the University of Pittsburgh suggests that the oft-repeated adage applies not just to physical health but to brain power as well.”

Forensic science solves mystery of Richard III’s death (the parking-lot king) –  Agata Blaszczak-Boxe – CBS News

“More than 500 years after Richard III became the last king of England to die in battle, researchers using modern forensic science have figured out which injuries likely caused his death.”

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General microbiology and science digest, September 16, 2014

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Detection of microbes in tissues, a magnet to pull out bacteria from blood, temperature stability of samples, enriching for rare microbial community members, bioinformatics tools for microbiome research, and Bik’s Picks.
Microbial detection

Metagenomic Assay for Identification of Microbial Pathogens in Tumor Tissues – Don A. Baldwin – mBio

“the PathoChip platform was developed by targeting viral, prokaryotic, and eukaryotic genomes with multiple DNA probes in a microarray format that can be combined with a variety of upstream sample preparation protocols and downstream data analysis. “

More microbes

Review: Physical stress and bacterial colonization – Michael Otto – FEMS Microbiology Reviews

“This review will give an overview over the mechanisms human bacterial colonizers have to withstand physical stresses with a focus on bacterial adhesion.”

Techniques

16S rRNA gene pyrosequencing of reference and clinical samples and investigation of the temperature stability of microbiome profiles – Jun Hang – Microbiome

“Three readily available mock bacterial community materials and two commercial extraction techniques, Qiagen DNeasy and MO BIO PowerSoil DNA purification methods, were used to assess procedures for 16S ribosomal DNA amplification and pyrosequencing-based analysis.”

Improving the genetic representation of rare taxa within complex microbial communities using DNA normalisation methods – Dragana Gagic – Molecular Ecology Resources

“The synthetic metagenome was fractionated and thermally re-natured, allowing the most abundant sequences to hybridise. Double-stranded DNA was removed either by hydroxyapatite chromatography, or by a duplex-specific nuclease (DSN).”

Bioinformatics

A better sequence-read simulator program for metagenomics – Stephen Johnson – BMC Bioinformatics

“We present BEAR (Better Emulation for Artificial Reads), a program that uses a machine-learning approach to generate reads with lengths and quality values that closely match empirically-derived distributions.”

Gene finding in metatranscriptomic sequences – Wazim Mohammed Ismail, Yuzhen Ye and Haixu Tang – BMC Bioinformatics

“In this paper, we present TransGeneScan, a software tool for finding genes in assembled transcripts from metatranscriptomic sequences.”

Data analysis for 16S microbial profiling from different benchtop sequencing platforms
Victor S. Pylro – Journal of Microbiological Methods

“Satisfactory results were obtained in those pipelines that applied a chimera-filtering step.”

Metagenome fragment classification based on multiple motif-occurrence profiles – Naoki Matsushita – PeerJ

“we have updated the Naïve Bayes Classifier method using multiple sets of occurrence profiles for each reference genome by normalizing the genome sizes, dividing each genome sequence into a set of subsequences of similar length and generating profiles for each subsequence.”

Revolutionizing prokaryotic systematics through next-generation sequencing – Vartul Sangal – Methods in Microbiology

“In this chapter, we have provided a brief summary of recent advances in sequencing technologies and easy to use bioinformatic tools to analyse sequence data, with a focus on prokaryotic biology. “

Microbes in the news

A Lesson in Language – McAlarnen, Lindsey A. – Academic Medicine

“while I expected a challenge working with human microbiome expert Dr. Rob Knight, I never expected to be as lost as I was that first morning.”

An extracorporeal blood-cleansing device for sepsis therapy – Joo H Kang – Nature Medicine

“Magnets pull the opsonin-bound pathogens and toxins from the blood; the cleansed blood is then returned back to the individual. “

Science and career

Too Few University Jobs For America’s Young Scientists – Richard Harris – NPR Morning Edition

“Imagine a job where about half of all the work is being done by people who are in training. That’s, in fact, what happens in the world of biological and medical research.”

Diversity in Science: Where Are the Data? – Fred Guterl – Scientific American

“Global figures on diversity in the science and engineering workforce are hard to come by, but what we know is not flattering”

 

Bik’s Picks

Jack the Ripper, more poison at NIH, Rosetta & the comet – Tabitha M. Powledge – PLOS Blogs

“Scientists have greeted with hoots and catcalls the claim that Jack the Ripper, the near-mythical late-19th Century London serial killer, has been identified from DNA as an immigrant Polish baker named Aaron Kosminski.”

Human faces are so variable because we evolved to look unique – ScienceDaily

“The amazing variety of human faces — far greater than that of most other animals — is the result of evolutionary pressure to make each of us unique and easily recognizable”

Joanne Chang Brings the Sweet Science of Sugar to Harvard – Leah Blumenthal – Eater.com

“Harvard University’s annual Science & Cooking public lecture series brings chefs from around the world to lecture on the intersection of science and cooking.”

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Animal microbiome digest, September 16, 2014

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Microbiomes of baby elephants, baby macaques, cows, mice, honey bees, oysters, Panama forest trees, yoghurt, air, beer, and clothes. We also learn that oregano has no effect on piglet microbiome. Just in case you wondered.

Mammal microbiome

A Comparative Metagenome Survey of the Fecal Microbiota of a Breast- and a Plant-Fed Asian Elephant Reveals an Unexpectedly High Diversity of Glycoside Hydrolase Family Enzymes – Nele Ilmberger – PLOS ONE

“A phylogenetic and metagenomic study of elephant feces samples (derived from a three-weeks-old and a six-years-old Asian elephant) was conducted in order to describe the microbiota inhabiting this large land-living animal.”

Breast-fed and bottle-fed infant rhesus macaques develop distinct gut microbiotas and immune systems – Amir Ardeshir – Science Translational Medicine

“We show that breast-fed and bottle-fed infant rhesus macaques develop markedly different immune systems, which remain different 6 months after weaning when the animals begin receiving identical diets.”

Characterization of the rumen lipidome and microbiome of steers fed a diet supplemented with flax and echium oil – Sharon Ann Huws – Microbial Biotechnology

“Microbiome pyrosequences showed that 50% of the bacterial genera were core to all diets (found at least once under each dietary intervention)”

Metagenome of Mehsani Buffalo Rumen Microbiota: An Assessment of Variation in Feed-Dependent Phylogenetic and Functional Classification – Parmar N.R. – Journal of Molecular Microbiology and Biotechnology

“Diet composed of varying proportion of green and dry roughages along with grains was given to 8 Mehsani buffaloes, and rumen metagenome was sketched using shotgun semiconductor sequencing.”

Gastrointestinal microbiota of wild and inbred individuals of two house mouse subspecies assessed using high throughput parallel pyrosequencing – Jakub Kreisinger – Molecular Ecology

“Using 454 pyrosequencing, we performed 16S rDNA GTM barcoding for 30 wild house mice (Mus musculus) and wild-derived inbred strain mice belonging to two subspecies (M.m.musculus and M.m. domesticus).”

The Use of Restriction Fragment Length Polymorphism and Fluorescence in Situ Hybridization to Investigate Microbiota of Piglets after Feeding Oregano – Katrin Stelter – Food and Nutrition Sciences

“The results showed no significant changes in microbiota in response to oregano. “

Insect microbiome

Buzz off, that’s my bee! – Gemma Langridge – Nature Reviews Microbiology

“These newly sequenced bee gut symbionts have revealed multiple genes that are candidates for determining host specificity. “

Hidden Diversity in Honey Bee Gut Symbionts Detected by Single-Cell Genomics – Philipp Engel – PLOS Genetics

“In both species, the divergence of 16S rRNA loci appears to have been curtailed by frequent recombination within populations, while other genomic regions have continuously diverged. “

Bacterial Communities in the Gut and Reproductive Organs of Bactrocera minax (Diptera: Tephritidae) Based on 454 Pyrosequencing – Ailin Wang – PLOS ONE

“We used a 454 pyrosequencing technology to study in depth the microbial communities associated with gut and reproductive organs of Bactrocera minax.”

Invertebrate microbiome

Hemolymph microbiome of Pacific oysters in response to temperature, temperature stress and infection – Ana Lokmer and Karl Mathias Wegner – ISME Journal

“We monitored oyster survival and repeatedly collected hemolymph of dead and alive animals to determine the microbiome composition by 16s rRNA gene amplicon pyrosequencing. “

Plant microbiome

Relationships between phyllosphere bacterial communities and plant functional traits in a neotropical forest – Steven W. Kembel – PNAS

“In this study we sequenced bacterial communities present on tree leaves in a neotropical forest in Panama, to quantify the poorly understood relationships between bacterial biodiversity on leaves (the phyllosphere) vs. host tree attributes. “

Litter decomposition and soil microbial community composition in three Korean pine (Pinus koraiensis) forests along an altitudinal gradient – Yong Zhou – Plant and Soil

“Single- and mixed-species litter decomposition rates were determined by the litterbag method and soil microbial community composition was characterized by PLFAs.”

Soil microbiome

Pyrosequencing assessment of rhizosphere fungal communities from a soybean field – Akifumi Sugiyama – Canadian Journal of Microbiology

“This study utilized 454 pyrosequencing to analyze rhizosphere fungal communities during soybean growth.”

Water microbiome

Seasonal and interannual variability of the marine bacterioplankton community throughout the water column over ten years – Jacob A Cram – ISME Journal

“Biodiversity appeared to be driven partially by exchange of microbes between depths and was highest when communities were changing slowly over time.”

Long-term effects of the antibacterial agent triclosan on marine periphyton communities – Martin Eriksson – PeerJ PrePrints

“Pollution-Induced Community Tolerance (PICT) was observed for algae and cyanobacteria at 100 nM TCS and higher.”

Review: Master recyclers: features and functions of bacteria associated with phytoplankton blooms – Alison Buchan – Nature Reviews Microbiology

“In this Review, we discuss the central role that these bacteria have in transforming phytoplankton-derived organic matter and thus in biogeochemical nutrient cycling.”

Built environment microbiome

Diversity and dynamics of the indoor air microbiome in an urban subway network – Marcus H. Y. Leung – Applied and Environmental Microbiology

“Targeting the 16S rDNA V4 region, extensive taxonomic diversity was found, with the most common bacterial genera in the subway environment among those seen associated on skin.”

Microbial Odor Profile of Polyester and cotton clothes after a fitness session – Chris Callewaert – Applied and Environmental Microbiology

“A dissimilar bacterial growth was found in cotton versus synthetic clothing textiles. Micrococci were isolated in almost all synthetic shirts and were detected almost solely on synthetic shirts by means of DGGE fingerprinting. “

Food microbiology

Vegetable microbiomes: is there a connection among opportunistic infections, human health and our ‘gut feeling’? – Gabriele Berg – Microbial Biotechnology

“Based on these results, we discuss the question if vegetables can serve as a source of infection for immunocompromised individuals as well as possible solutions to avoid outbreaks. “

Assessment of the bacterial and fungal diversity in home-made yoghurts of Xinjiang of China by pyrosequencing – Haiyan Xu – Journal of the Science of Food and Agriculture

“The bacterial and fungal community diversity of 22 home-made yoghurt samples from Zhaosu and Tekesi counties of Xinjiang in China were analyzed with pyrosequencing. “

Victory, life-sciences firm team up to detect bacteria that can spoil beer’s taste – Diane Mastrull – Philly.com

“The list is long of the perfect accompaniments to beer: hot dogs, pizza, peanuts, and pretzels, to name just a few. Most definitely not on that list: pediococcus and lactobacillus. Consider them beer buzzkills.”

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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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General microbiology and science, September 15, 2014

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Biodiversity and evolution in microbial communities, metabolomics, swabbing, DNA extraction, ITS approaches, marine viruses, and Bik’s Picks.

Microbial Ecology

The cryptic role of biodiversity in the emergence of host–microbial mutualisms – Pradeep Pillai – Ecology Letters

“Using a metacommunity model, we show that competition between multiple cheaters within the host’s microbiome, when combined with the spatial structure of host–microbial interactions, can have a constructive rather than a disruptive effect by allowing the emergence and maintenance of mutualistic microorganisms within the host.”

Microbial communities evolve faster in extreme environments – Sheng-Jin Li – Nature Scientific Reports

“Here we report a relative evolutionary rates (rERs) analysis of microbial communities from six diverse natural environments based on 40 metagenomic samples. “

Metabolomics

Mapping the Inner Workings of the Microbiome: Genomic- and Metagenomic-Based Study of Metabolism and Metabolic Interactions in the Human Microbiome – Ohad Manor, Roie Levy, Elhanan Borenstein – Cell Metabolism

“Here, we discuss recent efforts to study the metabolic inner workings of this complex ecosystem. “

Techniques

Comparison of seven methods for extraction of bacterial DNA from fecal and cecal samples of mice – Janina Ferrand – Journal of Microbiological Methods

“DNA quantity and quality were assessed by fluorometry, spectrophotometry, gel electrophoresis and qPCR….For both feces and intestinal contents, the most efficient extraction method was the FastDNA® SPIN Kit for Soil.”

Swab Sample Transfer for Point-Of-Care Diagnostics: Characterization of Swab Types and Manual Agitation Methods – Nuttada Panpradist – PLOS ONE

“In this study, we compared bacterial release efficiency of seven swab types using manual-agitation methods typical of POC devices.”

Improved resolution of bacteria by high throughput sequence analysis of the rRNA internal transcribed spacer – Paul M. Ruegger – Journal of Microbiological Methods

“Comparisons of the ITS region and two SSU regions using annotated bacterial genomes in GenBank showed much greater resolving power is possible with the ITS region. “

Pyroprinting: A rapid and flexible genotypic fingerprinting method for typing bacterial strains – Michael W. Black – Journal of Microbiological Methods

“Pyroprinting relies on the simultaneous pyrosequencing of polymorphic multicopy loci, such as the intergenic transcribed spacer regions of rRNA operons in bacterial genomes.”

Bioinformatics

OrthoClust: an orthology-based network framework for clustering data across multiple species – Koon-Kiu Yan – Genome Biology

“We demonstrate the application of OrthoClust using the RNA-Seq expression profiles of Caenorhabditis elegans and Drosophila melanogaster from the modENCODE consortium.”

Viruses and Phages

Review: Factors affecting virus dynamics and microbial host–virus interactions in marine environments – Kristina D.A. Mojica and Corina P.D. Brussaard – FEMS Microbiology Ecology

“The goal of the present minireview was to contribute to the evolution of marine viral ecology, through the assimilation of available data regarding the manner and degree to which environmental factors affect viral decay and infectivity as well as influence latent period and production.”

More Microbes

Dead or Alive: Molecular Assessment of Microbial Viability – Gerard A. Cangelosi and John S. Meschke – Applied and Environmental Microbiology

“This article reviews molecular viability analysis in that context and discusses future opportunities for these strategies in genetic, metagenomic, and single-cell microbiology.”

Bacteria in the news

Is your body mostly microbes? Actually, we have no idea – Peter Andrey Smith – The Boston Globe

“There’s only one problem: The oft-cited 10-to-1 figure is almost certainly inaccurate.”

The Death Microbiome Could Inform Forensic Science And Medicine – Randall Mayes – Design & Trend

“For pathologists working out the time of death, research has focused on the way that insects and microbes from a corpse’ environment take up residence in the flesh.”

Tiny hitchhikers, big health impact: Studying the microbiome to learn about disease – Krista Conger – ScopeBlog Stanford

Got microbes? Meet some of the tiny life forms that call you home and may make antibiotics for you (with annoying 5 questions if you want to read the whole article) – Susannah Bodman – Oregon Live

Fighting Poisons With Bacteria – Going Inside the Rice Microbiome – Carina Storrs – NY Times

“Dr. Bais is working to develop rice plants that take up less arsenic, a common contaminant in the fields of his native India and other Asian countries.”

Possum faeces may cause flesh-eating ulcers in humans, Victorian researchers say – ABC Australia

“Infectious disease researchers at Victoria’s Barwon Health have found that possums can carry the buruli bacteria, which can cause major skin ulcers in humans.”

Scientific publishing

Ten Simple Rules for Better Figures – Nicolas P. Rougier – PLOS Computational Biology

“we aim to provide a basic set of rules to improve figure design and to explain some of the common pitfalls.”

The digital toolbox – Nature Editorial

“A new section of Nature examines the software and websites that make research easier.”

Scientific career

There is life after academia – Nature Editorial

“With high numbers of postdocs emerging from universities, prospective PhD students must be prepared for the fact that they will probably not end up with a career in research.”

Bik’s Picks

PBS: Video on the science behind brewing beer hops to it – CNET

“PBS series “It’s Okay To Be Smart” takes a look at how beer is made, and what external factors influence the final product.”

The coffee genome provides insight into the convergent evolution of caffeine biosynthesis -France Denoeud – Science

“We generated a high-quality draft genome of the species Coffea canephora, which displays a conserved chromosomal gene order among asterid angiosperms. “

On the Other Hand – Bob Grant – The Scientist

“Handedness, a conspicuous but enigmatic human trait, may be shared by other animals. What does it mean for evolution and brain function?”

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Non-human microbiome digest, September 15, 2014

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Microbiomes of seals, sheep, pigs, raw milk, cheese, rubber, ocean, freshwater, acid mine drainage, deepsea basalt, and insects.

Mammal microbiome

Isolated faecal bacterial communities found for Weddell seals, Leptonychotes weddellii, at White Island, McMurdo Sound, Antarctica – Jonathan C. Banks – Polar Biology

“Here, we used 16S sequences obtained from clone libraries to characterise the faecal microbiota of Weddell seals breeding in McMurdo Sound and at White Island, Antarctica.”

Study of methanogen communities associated with different rumen protozoal populations – Alejandro Belanche – FEMS Microbiology Ecology

“Rumen protozoa were harvested from totally-faunated sheep and six protozoal fractions (plus free-living microbes) were generated by sequential filtration. “

Temporal changes and the effect of subtherapeutic concentrations of antibiotics in the gut microbiota of swine – Devin B. Holman and Martin R. Chénier – FEMS Microbiology Ecology

“In this study, the effect of two antibiotics on the swine gut microbiota over a 19-week monitoring period was investigated using Illumina-based sequencing.”

Development of a phylogenetic microarray for comprehensive analysis of ruminal bacterial communities – M. Kim – Journal of Applied Microbiology

“The utility of the RumenBactArray was tested using fractionated rumen samples obtained from sheep fed two different diets.”

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

“Fecal microbiota profiles were generated based on amplification and sequencing of the cpn60 universal target sequence from 89 samples from 18 pigs collected at −8, −5, −3 and 0 days post-inoculation, and at termination.”

Spatial heterogeneity of gut microbiota reveals multiple bacterial communities with distinct characteristics – Hsiao-Pei Lu – Scientific Reports

“We analyzed bacterial communities of six distinct gut sites (the food bolus and mucus layer of the proximal small intestine, cecum and distal large intestine), using wild folivorous flying squirrels.”

Insect microbiome

Dynamics of midgut microflora and dengue virus impact on life history traits in Aedes aegypti – Casey L. Hill – Acta Tropica

“Here we investigated the effects of the midgut microbial environment and dengue infection on several fitness characteristics among three strains of the primary dengue virus vector mosquito Aedes aegypti. “

Anterior Foregut Microbiota of the Glassy-Winged Sharpshooter Explored Using Deep 16S rRNA Gene Sequencing from Individual Insects – Elizabeth E. Rogers – PLOS ONE

“Here, a survey of microbiota associated with the GWSS anterior foregut was conducted.”

The bacterial microbiota of Stolotermes ruficeps (Stolotermitidae), a phylogenetically basal termite endemic to New Zealand – Nicola M. Reid – FEMS Microbiology Ecology

“We identified core bacterial taxa involved in gut processes through combined DNA- and RNA (cDNA)-based pyrosequencing analysis of 16S rRNA from five S. ruficeps colonies.”

Sponge and coral microbiome

Molecular diversity of fungal and bacterial communities in the marine sponge Dragmacidon reticulatum – Michel R. Z. Passarini – Journal of Basic Microbiology

“The present work aimed to investigate the diversity of bacteria and filamentous fungi of southern Atlantic Ocean marine sponge Dragmacidon reticulatum using cultivation-independent approaches.”

Host-specific microbial communities in three sympatric North Sea sponges – Mohd Azrul Naim – FEMS Microbiology Ecology

“In this study, we assessed the diversity of the microbial communities hosted by three sympatric sponges living in a semi-enclosed North Sea environment using pyrosequencing of bacterial and archaeal 16S ribosomal RNA gene fragments.”

Plant microbiome

Micro-organisms in latex and natural rubber coagula of Hevea brasiliensis and their impact on rubber composition, structure and properties – M. Salomez – Journal of Applied Microbiology

“This review synthesizes the current knowledge on microbial populations in latex and natural rubber coagula of H. brasiliensis and the changes they induce on the biochemistry and technical properties of natural rubber during maturation.”

Soils, sediments, and rocks microbiomes

A role for biotic filtering in driving phylogenetic clustering in soil bacterial communities – Marta Goberna – Global Ecology and Biogeography

“Here, we used phylogeny-based methods to discern whether the coexistence of evolutionarily related soil bacteria results from abiotic and/or biotic filtering.”

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

“..we investigated biogeochemical parameters and microbial community composition in a bog, a fen and two SSF using high throughput barcoded sequencing of the small ribosomal subunit (SSU) variable region V4.”

Deep-biosphere consortium of fungi and prokaryotes in Eocene subseafloor basalts – S. Bengtson – Geobiology

“We report here a consortium of fossilized prokaryotic and eukaryotic micro-organisms, occupying cavities in deep-drilled vesicular basalt from the Emperor Seamounts, Pacific Ocean, 67.5 m below seafloor (mbsf). “

Endolithic bacterial communities in rock coatings from Kärkevagge, Swedish Lapland – Cassandra L. Marnocha – FEMS Microbiology and Ecology

“Using 454 Roche pyrosequencing of the 16S rRNA gene, nine rock coating samples from three different coating mineralogies were sequenced. “

Water microbiome

Spatial and seasonal variation in diversity and structure of microbial biofilms on marine plastics in Northern European waters – Sonja Oberbeckmann – FEMS Microbiology Ecology

“Denaturing gradient gel electrophoresis (DGGE) and sequencing analysis revealed that plastisphere microbial communities on PET fragments varied both with season and location”

Biogeographic patterns in ocean microbes emerge in a neutral agent-based model – Ferdi L. Hellweger – Science

“We quantify the role of neutral processes by simulating division, mutation, and death of 100,000 individual marine bacteria cells with full 1 million–base-pair genomes in a global surface ocean circulation model. “

Microbial gardening in the ocean’s twilight zone: Detritivorous metazoans benefit from fragmenting, rather than ingesting, sinking detritus – Daniel J. Mayor – BioEssays

“Here we speculate that this apparently counterintuitive behaviour is an example of ‘microbial gardening’, a strategy that exploits the enzymatic and biosynthetic capabilities of microorganisms to facilitate the ‘gardener’s’ access to a suite of otherwise unavailable compounds that are essential for metazoan life.”

Diversity and spatiotemporal dynamics of bacterial communities: physicochemical and other drivers along an acid mine drainage – Aurélie Volant – FEMS Microbiology Ecology

“… biodiversity and spatiotemporal distribution of bacterial communities were characterized using T-RFLP fingerprinting and high-throughput sequencing. “

Diversity and activity of marine bacterioplankton during a diatom bloom in the North Sea assessed by total RNA and pyrotag sequencing – Anna Klindworth – Marine Genomics

“In this study we re-analyzed samples from the initial study by total community RNA (metatranscriptomics) and 16S rRNA gene amplicon sequencing.”

Effects of High Hydrostatic Pressure on Coastal Bacterial Community Abundance and Diversity – Angeliki Marietou and Douglas H. Bartlett – Applied and Environmental Microbiology

“Culturable high-pressure-surviving bacteria were obtained and found to be phylogenetically similar to isolates from cold and/or deep-sea environments. “

A high-throughput sequencing ecotoxicology study of freshwater bacterial communities and their responses to tebuconazole – Noémie Pascault – FEMS Microbiology Ecology

“Pyrosequencing revealed that bacterial diversity was higher in the river than in the lakes and in previously exposed sites than in pristine sites.”

Food Microbiology

Microbial Ecology Dynamics Reveal a Succession in the Core Microbiota Involved in the Ripening of Pasta Filata Caciocavallo Pugliese Cheese – Ilaria De Pasquale – Applied and Environmental Microbiology

“Pyrosequencing of the 16S rRNA targeting RNA, community-level physiological profiles made with Biolog EcoPlates, proteolysis, and volatile component (VOC) analyses were mainly used to characterize the manufacture and ripening of the pasta filata cheese Caciocavallo Pugliese.”

Tracing the origin of raw milk from farm by using Automated Ribosomal Intergenic Spacer Analysis (ARISA) fingerprinting of microbiota – Maria Feligini – Food Control

“A total of 64 markers within the range 279–756 bp were detected on the thirty-eight bulk milk samples, none of which was common to all the patterns. “

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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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