Category Archives: Food Microbiology

Microbiome digest, August 27, 2014

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

Pregnancy and birth 

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

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

Insect microbiome

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

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

Microbes in the news

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

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

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

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

Transcriptomics

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

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

Bik’s Picks

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

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

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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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Microbiome digest, August 21, 2014

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Ground squirrels, scallops, hypersaline water, and dead bodies.

Postmortem human microbiome

* Microbial communities associated with human decomposition and their potential use as postmortem clocks – Sheree J. Finley – International Journal of Legal Medicine

“the scope of this review is to provide a concise summary of the current progress in the newly emerging field of microbial diversity and the next-generation metagenomic sequencing approaches for assessing these communities in humans and in the soil beneath decomposing human.”

* Effects of Season and Host Physiological State on the Diversity, Density, and Activity of the Arctic Ground Squirrel Cecal Microbiota – Timothy J Stevenson – Applied and Environmental Microbiology

“We examined the seasonal changes of the cecal microbiota of captive arctic ground squirrels (Urocitellus parryii) by measuring microbial diversity and composition, total bacterial density and viability, and short-chain fatty acid concentrations at four sample periods (summer, torpor, interbout arousal, and posthibernation).”

Invertebrate microbiome

* IMMR abstract: Analysis of the scallop microbiota by means of 16S rRNA gene pyrosequencing – Aide Lasa – Frontiers in Microbiology

“In this study, we present the analysis of the microbiota associated to reared scallop gonads before and after spawning by pyrosequencing of the 16S rRNA gene. “

Soil microbiome

Bacterial diversity assessment in soil of an active Brazilian copper mine using high-throughput sequencing of 16S rDNA amplicons – Viviane D. Rodrigues – Antonie van Leeuwenhoek

“In this work, pyrosequencing of the V3 region of the 16S rDNA was used to analyze the bacterial communities in soil samples from a Brazilian copper mine. “

* Impact of long-term N, P, K, and NPK fertilization on the composition and potential functions of the bacterial community in grassland soil – Yao Pan – FEMS Microbiology Ecology

“Here, we applied DNA shotgun metagenomic techniques to investigate the effect of inorganic fertilizers N, P, K, and NPK on the bacterial community composition and potential functions in grassland soils in a 54-year experiment. “

Water microbiome

The Santa Pola saltern as a model for studying the microbiota of hypersaline environments – Antonio Ventosa – Extremophiles

“Multi-pond salterns constitute an excellent model for the study of the microbial diversity and ecology of hypersaline environments, showing a wide range of salt concentrations, from seawater to salt saturation. “

Food microbiology

Book: Microorganisms and Fermentation of Traditional Foods – Ramesh C. Ray, Montet Didier – CRC Press

Fungi

Reconstruction of the original mycoflora in pelleted feed by PCR-SSCP and qPCR – Samart Dorn-In – FEMS Microbiology Letters

“A fungal-specific primer pair ITS1/ITS5.8R was used to amplify fungal DNA; PCR products were processed for the PCR-SSCP method. In the resulting acrylamide gel, more than 85% of DNA bands of ground feeds were preserved after pelleting. “

 

From Dandruff to Deep-Sea Vents: Malassezia-like Fungi Are Ecologically Hyper-diverse – Anthony Amend – PLOS Pathogens

“As the dominant component of the mycobiota on human skin —both healthy and diseased [2] —the genus Malassezia has received a fair amount of attention. “

Microbes in the news

The Birth of Pathogens: How Bacteria Become Deadly – Brian Stallard – Nature World News

“Two new studies have revealed two very different ways bothersome bacteria strains can suddenly become deadly, evolving into difficult-to-rid pathogens that can threaten entire populations.” – belongs to a PNAS paper on Salmonella enterica, and a Nature Communications paper on Group B Streptococcus.

Bacteria colonies removed from Savannah River Site using special vacuum – Meg Mirshak – The Augusta Chronicle

“Scientists studied samples and determined the white, stringy “cobwebs” were made up of a broad variety of bacteria and a few types of microbes.”

ASU experts follow gut reaction in autism treatment study – Arizona State University

“A new study approved by the U.S. Food and Drug Administration and led by Arizona State University will examine a novel treatment – called fecal microbiota transplant (FMT) – for GI problems in children with autism.”

Science and career

Ailing academia needs culture change – Viviane Callier, Nathan L. Vanderford – Science

“The research enterprise has become unsustainable in its current form. Research funding levels/mechanisms, the peer-review process, and the methods of training Ph.D.’s are flawed, and these issues are crippling the pipeline of future, successful academic researchers”

Science Media Beset with Gender Gaps – By Curtis Brainard – Scientific American

“One antidote, summit participants suggested, would be having more reporters abide by the seven-part Finkbeiner Test”

Bik’s Picks

* Why does asparagus make our urine smell? – Claudia Hammond – BBC Future

“After eating asparagus, some people can detect a strange smell, while others claim not to notice a thing. What’s going on?”

Chemically mediated behavior of recruiting corals and fishes: A tipping point that may limit reef recovery – Danielle L. Dixson – Science

“We show that juveniles of both corals and fishes are repelled by chemical cues from fished, seaweed-dominated reefs but attracted to cues from coral-dominated areas where fishing is prohibited. “

Scientists discover how lizards regrow tails – John von Radowitz – The Independent

“Researchers have identified a genetic programme that triggers new tissue growth after a lizard sacrifices its tail to escape a predator.”

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Non-human microbiome, August 19, 2014

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A very diverse mix today: kangaroo, rumen, Daphnia, ticks, corals, rice, switchgrass, drinking water, acid mine drainage, rocks, soil microbiomes.

Mammal microbiome

* Investigation of the microbial metabolism of carbon dioxide and hydrogen in the kangaroo foregut by stable isotope probing – Scott Godwin – ISME Journal

“Our results clearly demonstrate that the activity of bacterial reductive acetogens is a key factor in the reduced methane output of kangaroos”

Temporal dynamics of fibrolytic and methanogenic rumen microorganisms during in situ incubation of switchgrass determined by 16S rRNA gene profiling – Hailan Piao – Frontiers in Microbiology

“Here we investigated the temporal succession of microbial taxa and its effect on fiber composition during rumen incubation using 16S rRNA amplicon sequencing.”

Arthropod microbiome

Bacterial epibionts of Daphnia: a potential route for the transfer of dissolved organic carbon in freshwater food webs – Ester M Eckert and Jakob Pernthaler – ISME Journal

“We analysed the activity and identity of bacterial epibionts in cultures of Daphnia galeata and of natural daphnid populations.”

Evaluation of microbial communities and symbionts in Ixodes ricinus and ungulate hosts (Cervus elaphus and Ovis aries) from shared habitats on the west coast of Norway
Erik G. Granquist – Ticks and Tick-borne Diseases

“Five different species; M. mitochondrii, W. pipientis, Borrelia spp., Rickettia spp. and A. phagocytophilum, were analyzed on a 7500 Fast Real-time PCR system (Life Technologies, Carlsbad, CA), and carried out in separate 96-wells reaction plates. “

Coral microbiome

New insights into Oculina patagonica coral diseases and their associated Vibrio spp. communities – Esther Rubio-Portillo – ISME Journal

“….we have analysed the seasonal patterns of the culturable Vibrio spp. assemblages associated with healthy and diseased O. patagonica colonies. “

Bloom of the cyanobacterium Moorea bouillonii on the gorgonian coral Annella reticulata in Japan – Hideyuki Yamashiro – Nature Scientific Reports

“In addition to the cyanobacterium–shrimp interaction, the new trait of anchoring by the cyanobacterium into gorgonian coral may contribute to persistence of this bloom.”

* Not just who, but how many: the importance of partner abundance in reef coral symbioses – Ross Cunning and Andrew C. Baker – Frontiers in Microbiology

“…we generate testable hypotheses regarding the importance of symbiont abundance by first discussing different metrics and their potential links to symbiosis performance and breakdown, and then describing how natural variability and dynamics of symbiont communities may help explain ecological patterns on coral reefs and predict responses to environmental change.”

Plant microbiome

Phylogeny and Functions of Bacterial Communities Associated with Field-Grown Rice Shoots – Takashi Okubo – Microbes and Environments

“Metagenomic analysis was applied to bacterial communities associated with the shoots of two field-grown rice cultivars, Nipponbare and Kasalath.”

Reviving of the endophytic bacterial community as a putative mechanism of plant resistance – Olga Podolich – Plant and Soil

“Based on the published results, we suggest that the endophyte-mediated stress tolerance or disease resistance can develop, if the plant hosts a sufficient diversity of ‘protective’ endophytes. “

The rhizosphere microbiota of plant invaders: an overview of recent advances in the microbiomics of invasive plants – Vanessa C. Coats, Mary E. Rumpho – Frontiers in Microbiology

“This review discusses recent advances in invasive plant biology that have resulted from microbiome analyses as well as the microbial factors that direct plant fitness and adaptability in natural systems.”

Kelp forest size alters microbial community structure and function on Vancouver Island, Canada – Jessica Liz Clasen and Jonathan B. Shurin – Ecology

“We investigated the response of microbial communities to variation in kelp abundance between regions with and without sea otter populations along the west coast of Vancouver Island, British Columbia, Canada”

Soil, sediments, rocks

* Impact of fire on active layer and permafrost microbial communities and metagenomes in an upland Alaskan boreal forest – Neslihan Taş – ISME Journal

“We measured geochemistry, GHG fluxes, potential soil enzyme activities and microbial community structure via 16SrRNA gene and metagenome sequencing.”

Integrated Metagenomics and Metatranscriptomics Analyses of Root-Associated Soil from Transgenic Switchgrass – Archana Chauhan – Genome Announcements

“Here we report metagenomic and metatranscriptomic analyses of root-associated soil from COMT switchgrass compared with nontransgenic counterparts.”

Abiotic stress tolerance and competition-related traits underlie phylogenetic clustering in soil bacterial communities – Marta Goberna – Ecology Letters

“We examined the distribution of 15 traits and 3290 bacterial taxa in 28 plots. Communities showed a marked functional response to the environment. “

Elevated nitrate enriches microbial functional genes for potential bioremediation of complexly contaminated sediments – Meiying Xu – ISME Journal

“Here we analyzed sediment microbial communities from a field-scale in situ bioremediation site, a creek in Pearl River Delta containing a variety of contaminants “

Occurrence and expression of bacterial human virulence gene homologues in natural soil bacteria – Ditte A. Søborg – FEMS Microbiology Ecology

“The presence and in vitro expression of homologues to 22 bacterial human virulence determinants amongst culturable soil bacteria was investigated.”

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

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

Biodegradation Potential of Organically Enriched Sediments under Sulfate- and Iron-Reducing Conditions as Revealed by the 16S rRNA Deep Sequencing – Tomoyuki Hori – Journal of Water and Environment Technology

“The effects of supplementation with sulfate and lepidocrocite (a crystalline Fe[III] oxide) on the structure and activity of the slurry microorganisms were examined by the combined physicochemical analyses and 16S rRNA deep sequencing. “

Soil bacterial diversity in degraded and restored lands of Northeast Brazil – Ademir Sérgio Ferreira Araújo – Antonie van Leeuwenhoek

“In this study we compare the structure and diversity of bacterial communities in degraded and restored lands in Northeast Brazil and determine the soil biological and chemical properties influencing bacterial communities. “

* Biogeochemical environments of streambed-sediment pore waters with and without arsenic enrichment in a sedimentary rock terrain, New Jersey Piedmont, USA
A.C. Mumford – Science of the Total Environment

“The 16S rRNA gene and the As(V) respiratory reductase gene, arrA, were amplified from DNA extracted from streambed pore water at both sites and analyzed, revealing that distinct bacterial communities that corresponded to the redox conditions were present at each site. “

Water, wastewater, sludge microbiome

* A comprehensive insight into bacterial virulence in drinking water using 454 pyrosequencing and Illumina high-throughput sequencing – Kailong Huang – Ecotoxicology and Environmental Safety

“In order to comprehensively investigate bacterial virulence in drinking water, 454 pyrosequencing and Illumina high-throughput sequencing were used to detect potential pathogenic bacteria and virulence factors (VFs) in a full-scale drinking water treatment and distribution system. “

A high-throughput sequencing ecotoxicology study of freshwater bacterial communities and their responses to tebuconazole – Pascault Noémie – 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.”

Disturbance and temporal partitioning of the activated sludge metacommunity – David C Vuono – ISME Journal

“Bacterial small subunit (SSU) rRNA genes were surveyed from sludge samples resulting in a sequence library of >417 000 SSU rRNA genes. “

Review: Environmental bacteriophages: viruses of microbes in aquatic ecosystems – Télesphore Sime-Ngando – Frontiers in Microbiology

“The present chapter sought to review the literature on the diversity and functional roles of viruses of microbes in environmental microbiology,”

* Inter-species interconnections in acid mine drainage microbial communities
Luis R. Comolli and Jill F. Banfield – Frontiers in Microbiology

“Here, we present cryogenic transmission electron microscope (cryo-TEM) 2D images and 3D tomographic datasets for archaeal species from natural acid mine drainage (AMD) microbial communities. “

A study on the microbial community structure in oil reservoirs developed by water flooding – Lin Junzhang – Journal of Petroleum Science and Engineering

“This study was performed to identify the microbial community structures in 10 different types of water-flooded oil reservoirs on Sinopec Shengli Oil Field. “

Microbes of the built environment

* Microbial Existence in Controlled Habitats and Their Resistance to Space Conditions – Kasthuri Venkateswaran – Microbes and Environments

“In this review, we discussed the presence of microbes in space research-related closed habitats and the resistance of some microbial species to the extreme environmental conditions of space.”

Microbial Monitoring of Crewed Habitats in Space—Current Status and Future Perspectives – Nobuyasu Yamaguchi – Microbes and Environments

“In this review, the current status of microbial monitoring conducted in the International Space Station (ISS) as well as the results of recent microbial spaceflight experiments have been summarized and future perspectives are discussed.”

Food microbiology

Investigation of bacterial and fungal diversity in tarag using high-throughput sequencing
Zhihong Sun – Journal of Dairy Science

“This is the first study on the bacterial and fungal community diversity in 17 tarag samples (naturally fermented dairy products) through a metagenomic approach involving high-throughput pyrosequencing. “

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Non-human microbiome, August 11, 2014

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Microbiomes of Eurasian Magpie, mosquitoes, ticks, 218 insect species, sponges, plants, and olives.

Bird microbiome

Effect of Incubation on Bacterial Communities of Eggshells in a Temperate Bird, the Eurasian Magpie (Pica pica) – Won Young Lee – PLOS ONE

“In this study, we employed culture-independent methods, quantitative PCR and 16S rRNA gene pyrosequencing, to elucidate the effect of incubation on the bacterial abundance and bacterial community composition on the eggshells of the Eurasian Magpie (Pica pica).”

Arthropod microbiome

Native microbiome impedes vertical transmission of Wolbachia in Anopheles mosquitoes
Grant L. Hughes – PNAS USA

“We show the native microbiota of Anopheles impede vertical transmission of Wolbachia. Antibiotic microbiome perturbation enables Wolbachia transmission in two Anopheles species.”

Microbial Population Analysis of the Salivary Glands of Ticks; A Possible Strategy for the Surveillance of Bacterial Pathogens – Yongjin Qiu – PLOS ONE

“Bacterial communities in each salivary gland were characterized by 16S amplicon pyrosequencing using a 454 GS-Junior Next Generation Sequencer. The Ribosomal Database Project (RDP) Classifier was used to classify sequence reads at the genus level. “

Insect Gut Bacterial Diversity Determined by Environmental Habitat, Diet, Developmental Stage, and Phylogeny of Host – Ji-Hyun Yun – Applied and Environmental Microbiology

In this study, we comprehensively characterized insect-associated gut bacteria of 305 individuals belonging to 218 species in 21 taxonomic orders, using 454 pyrosequencing of 16S rRNA genes.

Sponge microbiome

Genomic analysis reveals versatile heterotrophic capacity of a potentially symbiotic sulfur-oxidizing bacterium in sponge – Ren-Mao Tian – Environmental Microbiology

“Here, we present and analyze the first genome of sponge-associated SOB using a recently developed metagenomic binning strategy”

Plant microbiome

Foliage Friendships (behind paywall) – Peter Andrey Smith – Scientific American

“Microbial communities on a plant’s roots, stems and leaves may improve crop growth”

Effects of Fusarium oxysporum on rhizosphere microbial communities of two cucumber genotypes with contrasting Fusarium wilt resistance under hydroponic condition – Ju Ding – European Journal of Plant Pathology

“PCR-DGGE analysis of 16S rDNA fragments indicated that following FO inoculation, significant changes in the bacterial structure isolated from the root surfaces of susceptible plants were observed, such as an increased diversity index, a decreased evenness index, and the occurrence of several types of bacteria that decomposed organic substances.”

Food microbiology

Open-refrigerated retail display case temperature profile and its impact on product quality and microbiota of stored baby spinach – Liping Kou – Food Control

“All bags were immediately loaded in the display cases and the overall visual quality, tissue electrolyte leakage, total aerobic mesophilic bacteria and psychrotrophic bacteria were evaluated for each bag. “

Diversity and dynamics of the microbial community on decomposing wheat straw during mushroom compost production – Xi Zhang – Bioresouce Technology

“The development of communities of three important composting players including actinobacteria, fungi and clostridia was explored during the composting of wheat straw for mushroom production. “

Genetic diversity and dynamics of bacterial and yeast strains associated to Spanish-style green table-olive fermentations in large manufacturing companies – Helena Lucena-Padrós – International Journal of Food Microbiology

“We have genotyped a total of 1045 microbial isolates obtained along the fermentation time of Spanish-style green table olives from the fermentation yards (patios) of two large manufacturing companies in the province of Sevilla, south of Spain.”

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Microbiome Digest, August 1, 2014

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Microbiome composition and vaccine response or chemotherapy, cassava beer, two nice articles about metagenomics tools and contamination, and the weekend picks.

Human gut microbiome

Stool Microbiota and Vaccine Responses of Infants – M. Nazmul Huda – Pediatrics

“Actinobacteria abundance was positively associated with T-cell responses to BCG, OPV, and TT; with the delayed-type hypersensitivity response; with immunoglobulin G responses; and with TI. B longum subspecies infantis correlated positively with TI and several vaccine responses. “

Systematic review: the role of the gut microbiota in chemotherapy- or radiation-induced gastrointestinal mucositis – current evidence and potential clinical applications – Y. Touchefeu – Alimentary Pharmacology & Therapeutics

“Search of the literature published in English using Medline, Scopus and the Cochrane Library, with main search terms ‘intestinal microbiota’, ‘bacteremia’, ‘mucositis’, ‘chemotherapy-induced diarrhoea’, ‘chemotherapy-induced mucositis’, ‘radiotherapy-induced mucositis’.”

Food microbiology

Local domestication of lactic acid bacteria via cassava beer fermentation – Alese M. Colehour – PeerJ

“Bacteria responsible for chicha fermentation could be a source of microbes for the human microbiome, but little is known regarding the microbiology of chicha. “

Microbes in the News

It’s a bit – eh – graphic, but a nice overview of science and the people working in this field. I wish it would have contained a couple of pictures of non-pregnant women though. It feels as if we are only a vessel:  The Body’s Ecosystem – The Scientist

“Research on the human microbiome is booming, and scientists have moved from simply taking stock of gut flora to understanding the influence of microbes throughout the body.”

‘I’m not fat, it’s viral’ – Phage found in gut bacteria may aid obesity – Dan Stanton 0 Biopharma Reporter

“A newly discovered virus which infects intestinal bacteria might be a cause of obesity, but could increasing interest in bacteriophages drive new personalised medicines and alternatives to antibiotics?”

Diet Must be Different for Men and Women: Study – Soumo Ghosh – International Business Times

“The researchers found that the microscopic bacteria, or other such organism housed inside the human stomach are different in the case of men and women. Hence, they believe that the same diet for both may not have the same effect in them.”

Metabolomics

Emergent Biosynthetic Capacity in Simple Microbial Communities – Hsuan-Chao Chiu – PLOS Computational Biology

“Here we present a comprehensive computational framework, integrating high-quality metabolic models of multiple species, temporal dynamics, and flux variability analysis, to study the metabolic capacity and dynamics of simple two-species microbial ecosystems.”

Metagenomics

Metagenomics Mash-Up – Kelly Rae Chi – The Scientist

“The Scientist spoke with developers of tools for parsing genomic data from diverse communities of microorganisms. Here are some of the newest strategies and programs for taxonomic, functional, and comparative analyses.”

Microbial detection

Who are the contaminants in your sequencing project? – Jonathan Eisen – MicrobeNet

“Such amplification is alas pretty common – due to contamination occurring in some other material added to the PCR reaction. “

Science and publishing

The Self-Edited Woman – Paige Brown – SciLogs International

“Un-prompted, several young female science bloggers I’ve interviewed mention having blogged anonymously in the past, being self-conscious about expressing their expertise on a topic, or avoiding certain topics because of the nasty comments they might receive. “

Bik’s Picks

We have the science to build an Ebola vaccine. So why hasn’t it happened? – Sarah Kliff – Vox

“This isn’t how an Ebola outbreak has to work. Researchers have devoted lots of time to building a vaccine that could stop the disease altogether — and according to Daniel Bausch, a Tulane professor who researches Ebola and other infectious diseases, they’re making really significant progress.”

Littering and Following the Crowd – Vivian Wagner – The Atlantic

“Why it’s so tempting to throw trash on the ground, and how environmentalists are using psychology to change that”

F.D.A. Acts on Lab Tests Developed In-House – Andrew Pollack – The New York Times

“The Food and Drug Administration announced on Thursday that it would start regulating medical laboratory testing, saying that tests used to make important treatment decisions must be vetted and validated before they go into use.”

Grad Student Freed By Police After Three Years Trapped In The Same Experiment – The Allium

“He is thought to have survived by eating printouts of PloS One papers and drinking his own tears.”

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Non-human microbiome

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Microbiome of sheep, Drosophila on cherries, wild and sugar beets, sauerkraut, sake, and cheese. Sounds like a good meal.
Sheep microbiome

Pros and Cons of Ion-Torrent Next Generation Sequencing versus Terminal Restriction Fragment Length Polymorphism T-RFLP for Studying the Rumen Bacterial Community – Gabriel de la Fuente – PLOS ONE

“We analysed the bacterial diversity in the rumen of defaunated sheep following the introduction of different protozoal populations, using both next generation sequencing (NGS: Ion Torrent PGM) and terminal restriction fragment length polymorphism (T-RFLP).”

Insect microbiome

The bacterial communities of Drosophila suzukii collected from undamaged cherries
James Angus Chandler – PeerJ

“Using 16S rDNA PCR and Illumina sequencing, we characterized the bacterial communities of larval and adult D. suzukii collected from undamaged, attached cherries in California, USA. “

Evaluating Insect-Microbiomes at the Plant-Insect Interface – Clare L. Casteel, Allison K. Hansen – Journal of Chemical Ecology

“In this review, we critically evaluate the requirements for insect-associated microbes to develop synergistic relationships with their hosts, and we mechanistically discuss how some of these insect-associated microbes can target or modify host plant defenses.”

Saccharide breakdown and fermentation by the honey bee gut microbiome
Authors – Fredrick J. Lee – Environmental microbiology

“In order to better understand the contribution of the microbial community to food processing in the honey bee, we generated a metatranscriptome of the honey bee gut microbiome.”

Plant microbiome

Differences between the rhizosphere microbiome of Beta vulgaris ssp. maritima – ancestor of all beet crops – and modern sugar beets – Christin Zachow – Frontiers in Microbiology

“Therefore, we studied bacterial rhizosphere communities associated with the wild beet B. vulgaris ssp. maritima grown in their natural habitat soil from coastal drift lines (CS) and modern sugar beets (Beta vulgaris ssp. vulgaris) cultivated in CS and potting soil (PS) under greenhouse conditions.”

Endophytic bacterial community of grapevine leaves influenced by sampling date and phytoplasma infection process – Daniela Bulgari – BMC Microbiology

“Metagenomic DNA was extracted from sterilized leaves and the endophytic bacterial community dynamic and diversity were analyzed by taxon specific real-time PCR, Length-Heterogeneity PCR and genus-specific PCR. “

Water microbiology

Core Functional Traits of Bacterial Communities in the Upper Mississippi River Show Limited Variation in Response to Land Cover – Christopher Staley – Frontiers in Microbiology

“In this study we characterized functional microbial diversity at 11 sites along the Mississippi River in Minnesota using both metagenomic sequencing and functional-inference-based (PICRUSt) approaches.”

Potential drivers of microbial community structure and function in Arctic snow – Lorrie Maccario – Frontiers in Microbiology

“We applied a metagenomic approach to nine snow samples taken over two months during the spring season. Fungi, Bacteroidetes and Proteobacteria were predominant in metagenomic datasets and changes in community structure were apparent throughout the field season.”

Soil microbiology

Nutrient addition dramatically accelerates microbial community succession – Knelman JE – PLOS ONE

“We evaluated soil properties and examined bacterial community composition in plots before and one year after fertilization.”

Food microbiology

Sauerkraut: bacteria making food – S.E. Gould – Lab Rat – Scientific American

“As the bacteria required for sauerkraut fermentation are found on the cabbage leaves, it’s a very easy and healthy dish to produce. All you need is cabbage! “

Indigenous bacteria and fungi drive traditional kimoto sake fermentations
Nicholas A. Bokulich – Applied and Environmental Microbiology

“Results demonstrate a dynamic microbial succession, with koji and early moto fermentations dominated by Bacillus, Staphylococcus, and Aspergillus flavus subsp. oryzae, succeeded by Lactobacillus spp. and Saccharomyces cerevisiae later in the fermentations. “

Microbiota characterization of a Belgian protected designation of origin cheese, Herve cheese, using metagenomic analysis – V. Delcenserie – Journal of Dairy Science

“The aim of the study was to analyze the bacterial microbiota of Herve cheese using classical microbiology and a metagenomic approach based on 16S ribosomal DNA pyrosequencing. “

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Non-human microbiome, July 21

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Microbiomes of water fleas, marine zooplankton, soil, rumen, and how a microbiome can help woodrats eat toxic plants.

Rumen microbiome

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

“A total of 1,666 OTU-specific probes were designed and synthesized on microarray slides (referred to as RumenBactArray) in a 6×5k format with each probe being represented in triplicate.”

Rodent microbiome

Gut microbes of mammalian herbivores facilitate intake of plant toxins – Kevin D. Kohl – Ecology Letters

“We investigated the gut microbiota of desert woodrats (Neotoma lepida), some populations of which specialise on highly toxic creosote bush (Larrea tridentata). Here, we demonstrate that gut microbes are crucial in allowing herbivores to consume toxic plants. “

Crustacean microbiome

Water fleas require microbiota for survival, growth and reproduction – Marilou P Sison-Mangus – ISME Journal

“We assessed the effect of microbiota on Daphnia magna by experimentally depriving animals of their microbiota and comparing their growth, survival and fecundity to that of their bacteria-bearing counterparts.”

Soil microbiome

Soil Properties and Spatial Processes Influence Bacterial Metacommunities within a Grassland Restoration Experiment – Cheryl A. Murphy – Restoration Ecology

“We found that soil bacterial communities were not influenced by plant restoration, but rather, by the local heterogeneity of soil environmental properties (16.9% of bacterial community variation) and pure spatial effects (11.1%).”

Environmental drivers of soil microbial community distribution at the Koiliaris Critical Zone Observatory – Myrto Tsiknia – FEMS Microbiology Ecology

“This study investigates the distribution of archaea, bacteria and fungi as well as the dominant bacterial phyla (Acidobacteria, Actinobacteria, Bacteroidetes, Firmicutes), and classes of Proteobacteria (α- and β-Proteobacteria) across the Koiliaris watershed by qPCR and associate them with environmental variables. “

Soil microbial community structure and activity along a montane elevational gradient on the Tibetan Plateau – Meng Xu – European Journal of Soil Biology

“We investigated the microbial community composition and functional patterns along an elevational gradient (3100–4600 m above sea level) on Mount Segrila using phospholipid fatty acids (PLFAs) and community level physiological profiles (CLPP). “

Oil pipeline microbiome

Identification and characterization of microbial biofilm communities associated with corroded oil pipeline surfaces – Tiffany R. Lenhart – The Journal of Bioadhesion and Biofilm Research

“Eubacterial and archaeal 16S rRNA sequences of DNA recovered from extracted pipeline pieces, termed ‘cookies,’ revealed the presence of thermophilic sulfidogenic anaerobes, as well as mesophilic aerobes. “

Plankton microbiome

Zooplankton diversity across three Red Sea reefs using pyrosequencing – John K. Pearman – Frontiers in Marine Science

“The diversity of metazoan plankton was investigated by targeting the 18S rRNA gene and clustering OTUs at 97% sequence similarity. A total of 754 and 854 metazoan OTUs were observed in the data set for the 1380F and 1389F primer sets respectively. “

Food microbiology

Cheese Rind Communities Provide Tractable Systems for In Situ and In Vitro Studies of Microbial Diversity – Benjamin E. Wolfe – Cell

“Sequencing of 137 different rind communities across 10 countries revealed 24 widely distributed and culturable genera of bacteria and fungi as dominant community members. “

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General microbiology and science, July 16

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Comparison of 1700 metagenomes,  $125,000 to study 100 trillion bacteria, arsenic speciation, and the Seinfeld “double dipping” videoclip.

General microbiome and metagenome

Metagenome exploringExploring Neighborhoods in the Metagenome Universe – Kathrin P. Aßhauer – International Journal of Molecular Sciences

“Our evaluation on more than 1700 publicly available metagenomes indicates that for a query metagenome from a particular habitat on average nine out of ten nearest neighbors represent the same habitat category independent of the utilized profiling method or distance measure. “

UMass Cancer Avatar Institute, Center for Microbiome Research backed by UMass president

“Beth McCormick, PhD, professor of microbiology & physiological systems, was also awarded $125,000 to develop the Center for Microbiome Research, envisioned as a center of research and education for the microbiome, the ecosystem of the 100 trillion bacteria in the human body.”

Dengue virus

Endothelial Cells in Dengue Hemorrhagic Fever – Anon Srikiatkhachorn – Antiviral Research

“In this review we summarize dengue viruses and the spectrum of human disease and highlight evidence of endothelial cell dysfunction in DHF based on studies in patients and mouse and tissue culture models. “

Dengue fever and bone marrow myelofibrosis – Xin Qing – Experimental and Molecular Pathology

“We report the first case to our knowledge of myelofibrosis associated with dengue fever. We briefly describe dengue infections and hypothesize the causes of myelofibrosis in this condition.”

African genetic ancestry is associated with a protective effect on Dengue severity in colombian populations – Juan C. Chacón-Duque – Infection, Genetics and Evolution

“We found that African ancestry has a protective effect against severe outcomes under several systems of clinical classification”

Conference abstract: Longitudinal Analysis Of Dengue Fever Infections Reported In The Uk Betwen 2002 – 2013 Using The Health Improvement Network (Thin) Primary Care Database – D Ansell – Value in Health

Polio virus

Comment: Infectious disease: Polio eradication hinges on child health in Pakistan – Zulfiqar Ahmed Bhutta – Nature

“Last year, only 406 cases were reported, with 160 of them in just a few areas of the three countries where polio remains endemic”

Microbes in the news

Gut feeling: How intestinal bacteria may influence our moods – Sharon Oosthoek – CBC News

“Dr. Emeran Mayer, a gastroenterologist at University of California, Los Angeles, is a self-described sceptic, but admits “there is enough there to make me think some of the findings from animal studies can be extrapolated to humans.””

#BacteriaHysteria: Double-dipping spreads bacteria. But does it get people sick? (with the famous Seinfeld clip) – Joseph Stromberg – Vox.com

“Many people believe that dipping a chip into a shared bowl of drip, taking a bite, and dipping again — termed “double-dipping” in a 1993 episode of Seinfeld — is an abhorrently unsanitary practice. Others, like George Costanza, think this aversion is unscientific, and there’s actually no harm in double-dipping at all.”

Sizing up bacteria – Peter Reuell – Harvard Gazette

“A new theoretical framework outlined by a Harvard scientist could help solve the mystery of how bacterial cells coordinate processes that are critical to cellular division, such as DNA replication, and how bacteria know when to divide.”

Chilling new details on cold-storage smallpox – Hoai-Tran Bui and Alison Young, USA TODAY

Arsenic metabolism

arsenicComplementary Arsenic Speciation Methods: A Review – Michelle M. Nearing – Spectrochimica Acta Part B: Atomic Spectroscopy

“The toxicity of arsenic greatly depends on its chemical form and oxidation state (speciation) and therefore accurate determination of arsenic speciation is a crucial step in understanding its chemistry and potential risk.”

Science, ethics and publishing

Should Research Fraud be a Crime? A Reader Poll – Ed Silverman – Wall Street Journal

“A researcher may lose a job or stature, but should there be more serious consequences, such as criminal liability? A debate between two academics in BMJ, the British Medical Journal, explores the yin and yang surrounding this question.“

Dr. Bik’s Picks

Great title! IgG walkingIgGs are made for walking on bacterial and viral surfaces – Johannes Preiner – Nature Communications

“Here we utilize high-speed atomic force microscopy to examine the dynamics of antibody recognition and uncover a principle; antibodies do not remain stationary on surfaces of regularly spaced epitopes; they rather exhibit ‘bipedal’ stochastic walking”

Microbiome and general science digest, July 10

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Hi all, just one post today, with everything combined. Bacterial vaginosis, daily rhythms  of marine bacteria, food microbiology, and The Picks.

Human vaginal microbiome

Role of Gardnerella vaginalis in the Pathogenesis of Bacterial Vaginosis: A Conceptual Model – Jane R. Schwebke – Journal of Infectious Diseases

“Our model suggests that BV is initiated by the sexual transmission of Gardnerella vaginalis, which has the appropriate virulence factors to adhere to host epithelium, create a biofilm community, and successfully compete with lactobacilli for dominance in the vaginal environment. “

Seawater microbiome

Multispecies dielMultispecies diel transcriptional oscillations in open ocean heterotrophic bacterial assemblages – Elizabeth A. Ottesen – Science, with an Editorial by E. Virginia Armbrust: “Taking the pulse of ocean microbes”

“As anticipated, the cyanobacterial transcriptome exhibited pronounced diel periodicity. Unexpectedly, several different heterotrophic bacterioplankton groups also displayed diel cycling in many of their gene transcripts. “

Screen Shot 2014-07-10 at 11.53.04 PMReview: Bacterial diversity and antibiotic resistance in water habitats: searching the links with the human microbiome – Ivone Vaz-Moreira – FEMS Microbiology Reviews

“In this review, the hypothesis that some bacteria may share different water compartments and be also hosted by humans is discussed based on the comparison of the bacterial diversity in different types of water and with the human-associated microbiome. “

Food microbiology

Cassava beerLocal domestication of lactic acid bacteria via cassava beer fermentation – Alese M. Colehour – PeerJ

“Bacteria responsible for chicha fermentation could be a source of microbes for the human microbiome, but little is known regarding the microbiology of chicha. We investigated bacterial community composition of chicha batches using Illumina high-throughput sequencing. “

LobsterCharacterization of the dominant bacterial communities during storage of Norway lobster and Norway lobster tails (Nephrops norvegicus) based on 16S rDNA analysis by PCR-DGGE – Bekaert Karen – Food Microbiology

“To characterize as many bacterial species present as possible, we performed advanced molecular identification techniques (PCR-DGGE). The initial TVC of fresh Norway lobster meat was high (3.0 log cfu/g) as compared to fish.”

charquiEffect of autochthonous bacteriocin-producing Lactococcus lactis on bacterial population dynamics and growth of halotolerant bacteria in Brazilian charqui – Vanessa Biscola – Food Microbiology

“Charqui is a fermented, salted and sun-dried meat product, widely consumed in Brazil and exported to several countries. “

Microbes in the news

Using the gut microbiome to improve health – Mary MacVean – LA Times

“The “bistable” groups, the authors wrote, represent “tipping elements,” or components of the gut microbes that “exhibit alternative stable states linked to the overall ecosystem state and our physiology.” “

Science, Ethics and Publishing

Crack Down on Scientific Fraudsters – Adam Marcus and Ivan Oransky – New York Times

“Criminal charges against scientists who commit fraud are even more uncommon. In fact, according to a study published last year, “most investigators who engage in wrongdoing, even serious wrongdoing, continue to conduct research at their institutions.””

Dr. Bik’s Picks

Microplastics in the seas – Kara Lavender Law, Richard C. Thompson – Science

“Microplastics are likely the most numerically abundant items of plastic debris in the ocean today, and quantities will inevitably increase, in part because large, single plastic items ultimately degrade into millions of microplastic pieces. “

Uncontacted tribe in Brazil emerges from isolation – Heather Pringle – Science

“The meeting was Brazil’s first official contact with an isolated Amazonian tribe in 20 years. Anthropologists remain deeply concerned about the tribe’s future as it encounters novel diseases and resource-hungry outsiders. “

Polar BearsPolar Bears from Space: Assessing Satellite Imagery as a Tool to Track Arctic Wildlife – Seth Stapleton – PLOS ONE

“We examined satellite images of a small island in Foxe Basin, Canada, occupied by a high density of bears during the summer ice-free season. Bears were distinguished from other light-colored spots by comparing images collected on different dates. “

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