Category Archives: Human respiratory

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, August 28, 2014

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Cool new study today by Jack Gilbert on the bacteria living in our homes, what happens to you microbiome after you die, (gut) microbiome and respiratory diseases, lots of water studies, and Bik’s Picks.

General  human microbiome 

* Your death microbiome could catch your killer – Anna Williams – NewScientist

“These “friendly” bacteria adhere to the lining of the gut and keep the microbial villains at bay by outcompeting them. After we die, however, our gut flora have a party.“

Human respiratory microbiome

The Microbiome and the Lung – Lijia Cui – Annals of the American Thoracic Society

“In this review, we provide an overview of the basics of microbiome studies.”

Microbiome Diversity and Asthma and Allergy Risk – Antje Legatzki – Current Allergy and Asthma Reports

“In this review, we will discuss the available literature concerning the human microbiota and asthma and allergy development and occurrence. “

Gut microbiome

You waited for it: The journal Helicobacter has a Helicobacter special!
Gastric and Enterohepatic Helicobacters other than Helicobacter pylori –
Armelle Ménard – Helicobacter

“Several studies highlighted the virulence of non-H. pylori species including H. cinaedi in humans and hyperlipidemic mice or H. macacae in geriatric rhesus monkeys with intestinal adenocarcinoma. “

Pregnancy and birth

Systemic Inflammation in the Extremely Low Gestational Age Newborn Following Maternal Genitourinary Infections – Raina N. Fichorova – American Journal of Reproductive Immunology

“Mothers of 914 infants born before 28th gestation week reported cervical/vaginal infection (CVI), and/or urine/bladder/kidney infection (UTI), or neither. Inflammation proteins measured in baby’s blood”

Animal models of microbiome research

Intestinal Microbial Variation May Predict Early Acute Rejection after Liver Transplantation in Rats – Ren, Zhigang – Transplantation

“cluster analysis of denaturing gradient gel electrophoresis (DGGE) profiles showed the 7AR and 3AR groups clustered together with 73.4% similarity, suggesting that intestinal microbiota was more sensitive than hepatic function in responding to AR.”

Microbiology of the built environment

* Longitudinal analysis of microbial interaction between humans and the indoor environment – Simon Lax – Science

“Microbial communities associated with seven families and their homes over 6 weeks were assessed, including three families that moved their home. “

* Sloan Microbiology of the Built Environment Data Analysis Workshop (secrets of QIIME, VAMPS and QIITA) January 6-7, 2015 – Jonathan Eisen – MicroBEnet

“to learn hands-on how to use these tools on their own data, to perform meta-analyses that combine built environment datasets“

Water microbiome

Microbial weeds in hypersaline habitats: the enigma of the weed-like Haloferax mediterranei – Aharon Oren and John E. Hallsworth – FEMS Microbiology Letters

“Here, we discuss the enigma of the less abundant Haloferax mediterranei, an archaeon that grows faster than any other, comparable extreme halophile.”

Bacterial profiling in brine samples of the Emalahleni Water Reclamation Plant, South Africa, using 454-pyrosequencing method – Sudharshan Sekar – FEMS Microbiology Letters

“A metagenomic approach was applied using 454-pyrosequencing data analysis for the profiling of bacterial communities in the brine samples of the water reclamation plant. “

The role of dispersal mode and habitat specialisation in metacommunity structuring of aquatic macroinvertebrates in isolated spring fens – Vanda Rádková – Freshwater Biology

“We applied two species categorisations, common/rare and generalists/specialists, to disentangle the roles of dispersal capacity and habitat specialisation.”

Shifts in archaeaplankton community structure along ecological gradients of Pearl Estuary – Jiwen Liu – FEMS Microbiology Ecology

“Using 454 pyrosequencing, the present study examined the archaeal communities along a subtropical estuary, Pearl Estuary, China. “

Soil microbiome

The Effects of Radiation Pollution on the Population Diversities and Metabolic Characteristics of Soil Microorganisms – Meiying Gu – Water, Air, & Soil Pollution

“Microbial diversities were determined by using methods of cultured isolates and carbon source utilization on Biolog EcoPlate™. “

Bik’s Picks

A chocolate habit in ancient North America – Michael Bawaya – Science

“the findings suggest regular trade in cacao—and movements of the people who imbued it with significance—between ancient Mesoamericans and their northern neighbors, says Dorothy Washburn, an archaeologist at the University of Pennsylvania Museum of Archaeology and Anthropology “

Babies may be good at remembering, and forgetting – Laura Sanders – Science News

“over 20 percent of 5-year-olds and 8- to 9-year olds recounted events from their first year, some from the very first months of life.”

How the zebrafish gets its stripes: Uncovering how beautiful color patterns can develop in animals – Science Daily

“Three major pigment cell types, black cells, reflective silvery cells, and yellow cells emerge during growth in the skin of the tiny juvenile fish and arrange as a multi-layered mosaic to compose the characteristic color pattern. “

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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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Microbiome Digest, August 22, 2014

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The microbiome of the human eye,  chronic lung diseases, ticks, trout, the air in wineries, and Bik’s Picks. Have a good weekend!
Pregnancy and birth

The human microbiome and the great obstetrical syndromes, a new frontier in maternal fetal medicine – Ido Solt – Best Practice & Research Clinical Obstetrics & Gynaecology

“The transmission of maternal microbiomes to the neonate, according to vaginal delivery or cesarean section, is shown to affect health from birth to adulthood.”

Human skin microbiome

Considerations in Understanding the Ocular Surface Microbiome – Michael E. Zegans – American Journal of Ophthalmology

“In ophthalmology, the question naturally arises as to whether or not the ocular surface, like other mucous membrane surfaces, has a resident microbiota, and, if so, what role it plays in ocular surface physiology. This question has provoked much debate over many years. “

Human respiratory microbiome
* The role of the microbiome in exacerbations of chronic lung diseases – Robert P Dickson – The Lancet

“We propose that exacerbations are occasions of respiratory tract dysbiosis—a disorder of the respiratory tract microbial ecosystem with negative effects on host biology.”

Human gut microbiome

* Starving our Microbial Self: The Deleterious Consequences of a Diet Deficient in Microbiota-Accessible Carbohydrates – Erica D. Sonnenburg, Justin L. Sonnenburg – Cell Metabolism

“The low-MAC Western diet results in poor production of gut microbiota-generated short-chain fatty acids (SCFAs), which attenuate inflammation through a variety of mechanisms in mouse models. “

Human vaginal microbiome

Rectal Lactobacillus Species and Their Influence on the Vaginal Microflora: A Model of Male-to-Female Transsexual Women – Ljubomir Petricevic – The Journal of Sexual Medicine

“We undertook this observational study to characterize the Lactobacillus species present in the neovagina and rectum of male-to-female transsexual women and to determine the degree of neovaginal-rectal co-colonization in order to gain a better understanding of the potential role of the gut as a reservoir for genital lactobacilli.”

Animal models of microbiome research

Perinatal antibiotic-induced shifts in gut microbiota have differential effects on inflammatory lung diseases – Shannon L. Russell – Journal of Allergy and Clinical Immunology

“Disease severity was assessed by measuring lung inflammation, pathology, cytokine responses, and serum antibodies. Microbial community analyses were performed on stool samples via 16S ribosomal RNA pyrosequencing and correlations between disease severity and specific bacterial taxa were identified.”

Animal microbiome

The composition and transmission of microbiome in hard tick, Ixodes persulcatus, during blood meal – Xue-Chao Zhang – Ticks and Tick-borne Diseases

“By 16S rRNA Illumina sequencing, we investigated the microbiome of I. persulcatus and assessed the variation of the microbiome before and after blood feeding.”

Diet type dictates the gut microbiota and the immune response against Yersinia ruckeri in rainbow trout (Oncorhynchus mykiss) – Hans-Christian Ingerslev – Fish & Shellfish Immunology

“This study investigated the influence of the rainbow trout (Oncorhynchus mykiss) commensal intestinal microbiota in connection to an experimental Yersina ruckeri infection, the causative agent of enteric redmouth disease.”

Food microbiology

* Microbial communities in air and wine of a winery at two consecutive vintages – Fátima Pérez-Martín – International Journal of Food Microbiology

“The microbial composition was determined by using both a culture-dependent method and a culture-independent method, PCR-denaturing gradient gel electrophoresis (PCR-DGGE).”

Metabolomics

* Microbial catabolism of procyanidins by human gut microbiota – Keqin Ou – Molecular Nutrition & Food Research

“The objective of this study was to identify and quantify the microbial metabolites of procyanidins after anaerobic fermentation with human microbiota.”

Bioinformatics

* Defining the Estimated Core Genome of Bacterial Populations Using a Bayesian Decision Model – Andries J. van Tonder – PLOS Computational Biology

“The aim of our study was to develop a model to estimate the bacterial core genome from next-generation whole genome sequencing data and use this model to identify novel genes associated with important biological functions. “

* Comparative Analysis of Functional Metagenomic Annotation and the Mappability of Short Reads – Rogan Carr, Elhanan Borenstein – PLOS ONE

“Overall, our findings provide a first comprehensive evaluation of the capabilities and limitations of functional metagenomic annotation, providing crucial goal-specific best-practice guidelines to inform future metagenomic research.”

ExaBayes: Massively Parallel Bayesian Tree Inference for the Whole-Genome Era
Andre J. Aberer – Molecular Biology and Evolution

“We introduce a novel, user-friendly software package engineered for conducting state-of-the-art Bayesian tree inferences on datasets of arbitrary size.”

Microbes in the news

Behold 50 shades of Gross: A guide to Germaphobia! – Katherine Dahlhausen – MicroBEnet

“So logically, I began researching germaphobic practices. Some of them are just too good not to share! “

California Trees Nailed As The Source Of Mystery Infections – Nancy Shute – NPR

“”We had a good idea that the fungus was going to be associated with trees,” says Deborah Springer, a postdoctoral fellow at Duke University who studies C. gatti. “

Bik’s Picks

Pulling teeth from history: DNA from ancient teeth can help to yield information about our ancestors’ health, diet and diseases – Philip Hunter – EMBO Reports

“Teeth have proven to be an excellence source of ancient DNA. New analytical tools are helping to exploit this treasure trove to address questions about the link between diet and health, and the impact of historical epidemics with clear relevance for human health today.”

Ten Simple Rules of Live Tweeting at Scientific Conferences – Sean Ekins, Ethan O. Perlstein – PLOS Computational Biology

“Increasingly, some scientists are using Twitter as a vehicle to summarize presentations and posters at conferences in real time, which is defined as “live tweeting.””

Why the World Smells Different After It Rains – Behold, the wonders of petrichor.
Megan Garber – The Atlantic

“In the video above, PBS’s Joe Hanson describes the biology that leads to petrichor.”

Scientist Mistakenly Does “Dry-Ice Bucket Challenge” – The Allium

“Sad news has come to us today at The Allium, when we learned that scientist Dr. Liv Good, has mistakenly carried out a Dry-Ice Bucket challenge.”

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Human microbiome digest, August 19, 2014

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Lots of oral and gut microbiome papers today – Alzheimer’s, probiotics, chemotherapy and radiation.

Oral microbiome

Review: The Microbiome and Disease: Reviewing the Links between the Oral Microbiome, Aging, and Alzheimer’s Disease – Deborah K. Shoemark – Journal of Alzheimer’s Disease

“Evidence linking oral bacteria to Alzheimer’s disease (AD) is discussed in the context of aging, drawing together data from epidemiological, experimental, genetic, and environmental studies. “

* Human oral viruses are personal, persistent and gender-consistent – Shira R Abeles – ISME Journal

“To improve our understanding of the DNA viruses that inhabit the human oral cavity, we examined saliva from a cohort of eight unrelated subjects over a 60-day period. “

* Predictive modeling of gingivitis severity and susceptibility via oral microbiota – Shi Huang – ISME Journal

“In diseased plaque microbiota, 27 bacterial genera changed in relative abundance and functional genes including 33 flagellar biosynthesis-related groups were enriched.”

Phylogenetic and functional gene structure shifts of the oral microbiomes in periodontitis patients – Yan Li – ISME Journal

“Here, we examined the phylogenetic and functional gene differences between periodontal and healthy individuals using MiSeq sequencing of 16S rRNA gene amplicons and a specific functional gene array”

Perspective: Fungal-bacterial interactions and their relevance to oral health: linking the clinic and the bench – Patricia I. Diaz – Frontiers in Cellular and Infection Microbiology

“We highlight the need to conduct longitudinal clinical studies to simultaneously characterize the bacterial and fungal components of the human oral microbiome in health and during disease progression.”

Effect of an oxygenating agent on oral bacteria in vitro and on dental plaque composition in healthy young adults – Mercedes Fernandez y Mostajo – Frontiers in Cellular and Infection Microbiology

“During the experiment individuals used AX mouthwash twice daily in absence of other oral hygiene measures. The microbiological composition of plaque was assessed by 16S rRNA gene amplicon sequencing.”

* Review: Advancements toward a systems level understanding of the human oral microbiome
Jeffrey S. McLean – Frontiers in Cellular and Infection Microbiology

“This review will discuss some of the recent insights into the oral microbiome at a fundamental level, existing knowledge gaps, as well as challenges that have surfaced and the approaches to address them.”

Gut microbiome

* Xylan utilization in human gut commensal bacteria is orchestrated by unique modular organization of polysaccharide-degrading enzymes – Meiling Zhang – PNAS USA

“Here we demonstrate that two human gut commensal Bacteroides are equipped with unique enzymes that allow degradation of xylan, a common hemicellulose in human diets.”

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 hyper-variable region within the ITS suitable for precise taxonomic identification of all 48 so far recognized members of the Bifidobacterium genus.”

* Multi-omics analysis of Inflammatory Bowel Diseases – Hu Huang – Immunology Letters

“There is strong evidence of interactions between host genotype, environment, and gut microbiome profile in IBD.”

The methylome of the gut microbiome: disparate Dam methylation patterns in intestinal Bacteroides dorei – Michael T. Leonard – Frontiers in Microbiology

“Here metagenomic sequencing using the Pacific Biosciences platform allowed for rapid identification of bacterial GATC methylation status of a bacterial species in human stool samples. “

Perspective: Imposition of encapsulated non-indigenous probiotics into intestine may disturb human core microbiome – Abolfazl Barzegari – Frontiers in Microbiology

“..we envision that multi-probiotic therapy and holistic personalized microbiome supplements may be scientifically justified and valued in individualized probiotic designs and even targeted therapy of life-threatening diseases such as cancers in the future. “

Editorial: gut microbiota and chemotherapy- or radiation-induced gastrointestinal mucositis – M. R. Ferreira and H. J. N. Andreyev – Alimentary Pharmacology & Therapeutics

“Studies in those undergoing cancer therapy will lead to a new era in the treatment and prevention of the currently dreadful GI toxicity suffered by so many patients, and what we learn will almost certainly bring important insights to many other GI disorders.”

Respiratory microbiome

Cell-associated bacteria in the human lung microbiome – Robert P Dickson – Microbiome

“We present a novel methodological and analytical approach to the localization of lung microbiota and show that the prominent members of the lung microbiome are cell-associated, potentially via biofilms, cell adhesion, or intracellularity.”

Vaginal microbiome

A Systems Biology Approach Investigating the Effect of Probiotics on the Vaginal Microbiome and Host Responses in a Double Blind, Placebo-Controlled Clinical Trial of Post-Menopausal Women – Jordan E. Bisanz – PLOS ONE

“Analysis using 16S rRNA sequencing and metabolomics profiling revealed that the relative abundance of Lactobacillus was increased following probiotic administration as compared to placebo, which was weakly associated with an increase in lactate levels. “

Lactobacillus-dominated cervicovaginal microbiota associated with reduced HIV/STI prevalence and genital HIV viral load in African women – Hanneke Borgdorff – ISME Journal

“In this study, cervical samples of 174 Rwandan female sex workers were analyzed cross-sectionally using a phylogenetic microarray. “

* also tweeted by @MicrobiomDigest (yup, that’s me).

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Microbiome digest, August 13, 2014

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Nose, glycan, butyrate, microbes on plastics, seawater microbial mats, and plants with microbes.

Respiratory microbiome

The nasal cavity microbiota of healthy adults – Christine M Bassis, Alice L Tang, Vincent B Young and Melissa A Pynnonen – Microbiome

“In our initial analysis, we compared the bacterial communities of the nasal cavity and the oral cavity from ten of these subjects.”

Gut microbiome

Glycan Degradation (GlyDeR) Analysis Predicts Mammalian Gut Microbiota Abundance and Host Diet-Specific Adaptations – Omer Eilam – mBio

“Based on GlyDeR, we found a clear connection between microbial glycan degradation and human diet, and we suggest a method for the rational design of novel prebiotics.”

Microbial-Derived Butyrate: An Oncometabolite or Tumor-Suppressive Metabolite? -Scott J. Bultman, Christian Jobin – Cell Host & Microbe

“Dietary factors, microbial composition, and metabolism are intimately intertwined into a complex network whose activities influence important intestinal functions”

Review: Collateral Damage: Microbiota-Derived Metabolites and Immune Function in the Antibiotic Era – Christopher A. Lopez – Cell Host & Microbe

“A disruption of gut-associated microbial communities by antibiotic treatment can result in a depletion of microbiota-derived metabolites, thereby enhancing pathogen susceptibility, impairing immune homeostasis, and contributing to the rise of certain chronic inflammatory diseases”

Animal model of microbiome

Differential Modulation by Akkermansia muciniphila and Faecalibacterium prausnitzii of Host Peripheral Lipid Metabolism and Histone Acetylation in Mouse Gut Organoids
Sabina Lukovac – mBio

“The aim of this study was to characterize effects of the microbiota on host epithelium using a novel ex vivo model based on mouse ileal organoids.”

Plant microbiome

Phyllosphere Microbiota Composition and Microbial Community Transplantation on Lettuce Plants Grown Indoors – Thomas R. Williams, Maria L. Marco – mBio

“We found that Romaine lettuce grown in the laboratory contained 10- to 100-fold lower numbers of bacteria than age-matched, field-grown lettuce.”

Fundamental Plant Chemicals Rooted in Bacteria – Jenna Iacurci – Nature World News

“A fundamental chemical pathway that all plants use to create the essential amino acid phenylalanine has now been traced to two groups of ancient bacteria, a new study reports.”

Water microbiome

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

“Denaturing Gradient Gel Electrophoresis (DGGE) and sequencing analysis revealed that plastisphere microbial communities on PET fragments varied both with season and location, and comprised of bacteria belonging to Bacteroidetes, Proteobacteria, Cyanobacteria and members of the eukaryotes Bacillariophyceae and Phaeophyceae. “

Molecular Ecology of Microbial Mats – Henk Bolhuis – FEMS Microbial Ecology

“Here, we summarize some of the latest developments in metagenomic analysis of three representative phototrophic microbial mat types (coastal, hot spring and hypersaline).”

Microbes in the news

Wearable structure of bacteria references antique animal bone corsets

“in terms of the material, it is grown from acetobacter xylinum, a strain of bacteria that produces a microbial cellulose textile as it consumes glucose.”

Bik’s Picks

Google Maps Dives Underwater – Scientific American

“Google has taken its ‘street view’ maps to a whole new level—namely, the ocean’s depths. “

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Human microbiome, August 11, 2014

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Microbiome of Hadza Hunter, the premature infant gut, neonatal sepsis, skin and respiratory microbiome.

Microbiome general

BacterioFiles 178 – Hadza Hunters Have Heterogeneous Helpers (14 min) – Jesse Noar – BacterioFiles

“This episode: Modern hunter-gatherers have very different gut microbes from people from agricultural societies! “

“What is the FDA Going to Think?” – Negotiating Values through Reflective and Strategic Category Work in Microbiome Science – Katherine W. Darling – Science, Technology & Human Values

“Here, we describe how values are conceptualized and negotiated within microbiome research.”

Pregnancy and Birth microbiome

Patterned progression of bacterial populations in the premature infant gut – Patricio S. La Rosa – PNAS USA

“We demonstrate via 16S rRNA gene pyrosequencing of 922 specimens from 58 subjects that the gut microbiota of premature infants residing in a tightly controlled microbial environment progresses through a choreographed succession of bacterial classes“

Development of a multiplex real-time PCR assay for the rapid diagnosis of neonatal late onset sepsis – Marre van den Brand – Journal of Microbiological Methods

“we developed a real-time multiplex PCR assay tailored to LOS diagnosis which is easy-to-use, is applicable on small blood volumes and provides species-specific results within 4 h.”

Respiratory microbiome

Uncovering the hidden villain within the human respiratory microbiome – Chun Kiat Lee, Stephen James Bent – Diagnosis

“The review herein presents the current status of human airway microbiome research and highlights potential gaps which can be translated into research possibilities for future work on respiratory tract infection diagnosis”

Skin microbiome

The skin microbiome: potential for novel diagnostic and therapeutic approaches to cutaneous disease – Elizabeth A. Grice – Skin and Allergy News

“It is increasingly apparent that this collective set of microorganisms and their genetic material, the “microbiome”, contributes genetic diversity, modulates disease, influences metabolic processes, and is essential for immunity.”

Animal models of human microbiome

Citrobacter rodentium: infection, inflammation and the microbiota – James W. Collins – Nature Reviews Microbiology

“In this Review, we discuss recent studies in which C. rodentium has been used to study mucosal immunology, including the deregulation of intestinal inflammatory responses during bacteria-induced colitis and the role of the intestinal microbiota in mediating resistance to colonization by enteric pathogens. “

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Human microbiome digest, August 5, 2014

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Lots of microbiome papers today, so I will split it up into three posts. Here you will find papers on human gut, respiratory, oral, and vaginal microbiomes, as well as animal models.

Pregnancy and Birth

Prevalence and Clinical Significance of Sterile Intra-amniotic Inflammation in Patients with Preterm Labor and Intact Membranes – Roberto Romero – American Journal of Reproductive Immunology

“The purpose of this study was to (i) determine the prevalence and clinical significance of sterile intra-amniotic inflammation and (ii) examine the relationship between amniotic fluid (AF) concentrations of high mobility group box-1 (HMGB1) and the interval from amniocentesis to delivery in patients with sterile intra-amniotic inflammation.”

A Holobiont Birth Narrative: The Epigenetic Transmission of the Human Microbiome –
Scott F. Gilbert – Frontiers in Genetics

“Birth is nothing less than the passage from one set of symbiotic relationships to another.”

Fecal Short Chain Fatty Acids of Very Low Birth Weight Preterm Infants Fed Expressed Breast Milk or Formula – Pourcyrous, M.; Nolan, V.G.; Goodwin, A.; Davis, S.L.; Buddington, R.K. – Journal of Pediatric Gastroenterology & Nutrition

“ Ion chromatography was used to measure fecal SCFAs (acetate, formate, propionate, butyrate, and isobutyrate), lactate, and chloride in fresh stool samples collected from 32 preterm infants”

Human mouth microbiome

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

“DNA was directly extracted from each sample and the microbial composition was comprehensively analyzed using clone library analysis of the 16S rRNA gene”

 Respiratory microbiome

A large genomic island allows Neisseria meningitidis to utilize propionic acid, with implications for colonization of the human nasopharynx – Maria Chiara E. Catenazzi, Helen Jones, Iain Wallace, Jacqueline Clifton, James P. J. Chong, Matthew A. Jackson, Sandy Macdonald, James Edwards andJames W. B. Moir – Molecular Microbiology

“Data from classical microbiological and sequence-based microbiome studies provide several lines of supporting evidence that N. meningitidis colonization is correlated with propionic acid generating bacteria, with a strong correlation between prp-containing Neisseria and propionic acid generating bacteria from the genus Porphyromonas, and that this may explain adolescent/adult colonization by N. meningitidis.”

Analysis of Culture-Dependent vs. Culture-Independent Techniques for the Identification of Bacteria in Clinically-Obtained Bronchoalveolar Lavage Fluid – Robert P. Dickson – Journal of Clinical Microbiology

“We analyzed forty six clinically-obtained bronchoalveolar lavage (BAL) specimens from symptomatic and asymptomatic lung transplant recipients both by culture (using a clinical microbiology laboratory protocol) and by bacterial 16S rRNA gene pyrosequencing. “

Vaginal microbiome

Differences in vaginal microbiome in African American women versus women of European ancestry – Jennifer M. Fettweis – Microbiology

“we performed 16S rRNA gene survey to compare the microbiomes of vaginal samples from 1,268 African American women and 416 women of European ancestry. Our results confirmed significant differences in the vaginal microbiomes of the two groups and identified several taxa relevant to these differences.”

Human gut microbiome

Unraveling the mechanisms underlying associations between the microbiome and gastrointestinal malignancies – Tiffany L. Weir – Translational Gastrointestinal Cancer

“While many reviews have focused on research identifying microbial signatures associated with malignancies, including changes in diversity or evenness of GI microbial communities and depletion or overrepresentation of particular bacterial groups; this comprehensive review emphasizes research that explores the cause rather than effects of microbe-malignancy relationships.”

Animal models of human microbiome

Transfer of gut microbiota from lean and obese mice to antibiotic-treated mice – Merete Ellekilde, Ellika Selfjord, Christian S. Larsen, Maja Jakesevic, Ida Rune, Britt Tranberg, Finn K. Vogensen, Dennis S. Nielsen, Martin I. Bahl, Tine R. Licht, Axel K. Hansen & Camilla H. F. Hansen – Nature Scientific Reports

“To date, most studies of gut microbiota transfer are performed in germ-free mice. In the studies presented, it was tested whether an antibiotic treatment approach could be used instead. “

Postnatal Prebiotic Fiber Intake in Offspring Exposed to Gestational Protein Restriction Has Sex-Specific Effects on Insulin Resistance and Intestinal Permeability in Rats – Megan C. Hallam and Raylene A. Reimer – Journal of Nutrition

“At 24 wk of age, glucose tolerance, body composition, satiety hormones, gut microbiota, and markers of intestinal permeability were measured in the offspring. “

A polyphenol-rich cranberry extract protects from diet-induced obesity, insulin resistance and intestinal inflammation in association with increased Akkermansia spp. population in the gut microbiota of mice – Fernando F Anhê – Gut

“CE exerts beneficial metabolic effects through improving HFHS diet-induced features of the metabolic syndrome, which is associated with a proportional increase in Akkermansia spp. population.”

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Microbiome digest, August 4, 2014

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Relief in a pressing problem, microbes at high altitude, and microbiome in cystic fibrosis.

Human gut microbiome

So glad this one finally came out!  Structural changes in the gut microbiome of constipated patients – Lixin Zhu – Physiological Genomics

“A cross-sectional pilot study was performed to compare stool microbial composition of 8 constipated patients and 14 non-constipated controls using 16S rRNA gene pyrosequencing.”

Microbiota and diabetes: an evolving relationship – Herbert Tilg, Alexander R Moschen – Gut

“A further hint towards an association between microbiota and T2D has been derived from studies in pregnancy showing that major gut microbial shifts occurring during pregnancy affect host metabolism.”

Harnessing the Intestinal Microbiome for Optimal Therapeutic Immunomodulation – S. Viaud – Cancer Research

“gut commensals, through lipopolysaccharide and other bacterial components, switch the tumor microenvironment, in particular the redox equilibrium and the TNF production of intratumoral myeloid cells during therapies with platinum salts or intratumoral TLR9 agonists combined with systemic anti-IL10R Ab respectively.”

Specific genetic and microbial signature associated with paediatric ileal Crohn’s disease -Isobel Leake – Nature Reviews Gastroenterology & Hepatology

“An increase in DUOX2 expression was associated with an expansion of Proteobacteria across all forms of IBD, whereas downregulation of APOA1 expression in association with depletion of certain Firmicutes and Bacteroidetes taxa was found to be specific for Crohn’s disease.”

Skin and wounds microbiome

Next-Generation Sequencing: A Review of Technologies and Tools for Wound Microbiome Research – Brendan Hodkinson and Elizabeth Grice – Advances in Wound Care

“The purpose of this review is to outline the current platforms, their applications, and the steps necessary to undertake microbiome studies using next-generation sequencing.”

Human respiratory microbiome

Directly Sampling the Lung of a Young Child with Cystic Fibrosis Reveals Diverse Microbiota – Perry S Brown – Annals ATS

“After pathologic examination verified that this child’s lung tissue reflected CF lung disease, we used bacterial rRNA gene pyrosequencing and computational phylogenetic analysis to identify the microbiota in serial sections of the tissue.”

Respiratory Viruses and Bacteria among Pilgrims during the 2013 Hajj – Samir Benkouiten – Emerging Infectious Diseases

“One third (36.3%) of the participants had acquired S. pneumoniae during their stay. Our results confirm high acquisition rates of rhinovirus and S. pneumoniae in pilgrims and highlight the acquisition of coronavirus E229.”

Fish microbiome

The Colonization Dynamics of the Gut Microbiota in Tilapia Larvae – Christos Giatsis – PLOS ONE

“Our results showed that variation in gut microbiota between replicate tanks was not significantly higher than within tank variation, suggesting that there is no tank effect on water and gut microbiota. “

Soil microbiome

FEMS Microbiology Ecology has a special issue on Polar and Alpine Microbiology with many papers on microbiomes of ice and soil. Here is the Editorial:
Polar and alpine microbiology in a changing world – John C. Priscu – FEMS Microbiology Ecology

“By virtue of their relatively rapid growth rates and metabolic diversity, we can expect microorganisms to be the first responders to fluctuating climatic conditions.”

Altitudinal Distribution Patterns of Soil Bacterial and Archaeal Communities Along Mt. Shegyla on the Tibetan Plateau – Jun-Tao Wang – Microbial Ecology

“Our results found that the ratio of bacterial to archaeal 16S rRNA gene abundance was negatively related with elevation.”

Water microbiome

Satellite remote sensing data can be used to model marine microbial metabolite turnover – Peter E Larsen – ISME Journal

“We extrapolated marine surface microbial community structure and metabolic potential from 72 16S rRNA amplicon and 8 metagenomic observations using remotely sensed environmental parameters”

Microbial Ecology

Changes in community assembly may shift the relationship between biodiversity and ecosystem function – Joseph E. Knelman and Diana R. Nemergut – Frontiers Microbiology

“Can differences in community assembly alter the relationship between biodiversity and ecosystem function?”

Probiotics

Lactobacillus rhamnosus GG suspected infection in a newborn with intrauterine growth restriction – I. Sadowska-Krawczenko – Beneficial Microbes

“Genotyping with the rep-PCR and AFLP methods confirmed the 100% genetic similarity for both the strain isolated from patient blood and the probiotic product.”

Can Eating Probiotic Yogurt Help Lower Your High Blood Pressure? – Susmita Baral – Wall St Cheat Sheet

“Now, a new study (published Monday in the journal Hypertension) has found another added benefit of probiotics — it may reduce high blood pressure.”

Microbes in the News

Your garden hose: a potential health risk due to Legionella spp. growth facilitated by free-living amoebae – Jacqueline Marie Thomas – Environmental Science & Technology

“Here we present data on FLA and Legionella spp. detected in water and biofilm of two garden hose types over 18 months. “

Truth about your toothbrush – Anne Agbaje – Bussiness Day Online

“You don’t store your plates and glasses by the toilet, so why would you want to place your toothbrush there?” McCombs says. “It’s just common sense to store your toothbrush as far away from the toilet as possible.”

Metabolomics

Fecal volatile organic compounds: a novel, cheaper method of diagnosing inflammatory bowel disease? – Chris SJ Probert – Expert Review of Clinical Immunology

“…this article will focus specifically on the fecal VOC metabolome and its potential role in identifying a novel diagnostic method for IBD.”

Review: Emerging mass spectrometry techniques for the direct analysis of microbial colonies – Jinshu Fang, Pieter C Dorrestein – Current Opinion in Microbiology

“In this review/perspective, we illustrate the emerging mass spectrometry methodologies that enable the interrogation of specialized metabolites directly from microbial colonies.”

Techniques

Improved performance of the PacBio SMRT technology for 16S rDNA sequencing – Jennifer J. Mosher – Journal of Microbiological Methods

“With accurate read lengths of > 1400 base pairs, the PacBio system opens up the possibility of identifying microorganisms to the species level in environmental samples.”

 

Bik’s Picks

The Secret to a Tattoo’s Permanence: The Immune System – Olga Khazan – The Atlantic

“We rarely stop and think about the science of tattoos. In fact, some people don’t even stop and think before getting tattooed.”

 

Mathematical equation to predict happiness: Doesn’t depend on how well things go, but on whether things are better than expected – Science Daily

“The happiness of over 18,000 people worldwide has been predicted by a mathematical equation, with results showing that moment-to-moment happiness reflects not just how well things are going, but whether things are going better than expected.”

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