August 23, 2019

Good morning everyone!

This post is written from lovely NYC, quite a distance from my hometown in Israel. If you’re working on microbial ecology in the city and care for a cup of coffee (on me!) and a rather interesting chat about science, entreprenurship and agriculture- please contact me via barakdror@outlook.com or just find me on Linkedin.

Today post will feature highly recommended podcast, a great antimicrobial resistance review paper, Cocaine effect on gut microbiota, some cool bioinformatics tools papers, fascinating animal microbiome studies and more.

Resources and Podcast

I’m a huge fan of the This Week in Microbiology podcast. On their 201 episode the team hosted Prof. Mark Martin (U of Puget Sound) with some great list of papers for 1st year undergrads- but it is a great opportunity to read about general concepts and direction in micrboiology. I truely enjoed both the episode and the recommended papers.

15 Biotech-Themed Online Courses to Try at Home

Antibiotic Resistance

Defining and combating antibiotic resistance from One Health and Global Health perspectives, Sara Hernando-Amado, Nature Microbiology

Bioinformatics

An expectation-maximization algorithm enables accurate ecological modeling using longitudinal microbiome sequencing data, Chenhao Li, Microbiome

Analysing complex metagenomic data with MicroWineBar, Franziska Klincke ,bioRxiv

A systematic NGS-based approach for contaminant detection and functional inference, Sung-Joon Park, bioRxiv

Human and Animal microbiome

Cocaine Induces Inflammatory Gut Milieu by Compromising the Mucosal Barrier Integrity and Altering the Gut Microbiota Colonization, Ernest T. Chivero, Scientific Reports

Influence of the microbiota-gut-brain axis on behavior and welfare in farm animals: A review, Narjis Kraimi, Physiology & Behavior

Dissecting the factors shaping fish skin microbiomes in a heterogeneous inland water system, Yaron Krotman, bioRxiv

Non‐random associations of maternally transmitted symbionts in insects: The roles of drift versus biased co‐transmission and selection, Hugo Mathe-Hubert, Molecular Ecology

The microbiome of the Melitaea cinxia butterfly shows marked variation but is only little explained by the traits of the butterfly or its host plant, G. Minard, Environmental Microbiology

Food microbiome

The occurrence of Listeria monocytogenes is associated with built environment microbiota in three tree fruit processing facilities, Xiaoqing Tan, Microbiome

Environmental microbiome

Marine-freshwater prokaryotic transitions require extensive changes in the predicted proteome, Pedro J. Cabello-Yeves, Microbiome

Taxonomic and functional characterization of a microbial community from a volcanic englacial ecosystem in Deception Island, Antarctica, Emma Martinez-Alonso, Scientific Reports

Microbiome digest, October 16, 2014

Lung microbiome and pneumonia, bacterial vaginosis, microbiome and jetlag, cardiovascular consequences of gut dysbiosis, bacteria in locust guts and cropland in China, and how to earn some $$$ with your poop.

Human 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.”

Human vaginal microbiome

Recent progress in understanding the epidemiology of bacterial vaginosis – Kenyon, Chris R.; Osbak, Kara – Current Opinion in Obstetrics & Gynecology

“Bacterial vaginosis epidemiology has been transformed by new theoretical insights and methodologies, such as molecular sequencing. We summarize the progress made in these domains.”

Human gut microbiome

Transkingdom Control of Microbiota Diurnal Oscillations Promotes Metabolic Homeostasis – Christoph A. Thaiss – Cell

“Consequently, jet-lag-induced dysbiosis in both mice and humans promotes glucose intolerance and obesity that are transferrable to germ-free mice upon fecal transplantation.”

Far from the Eyes, Close to the Heart: Dysbiosis of Gut Microbiota and Cardiovascular Consequences – Matteo Serino – Current Cardiology Reports

“Here, we report evidence from the literature, as well as a few controversial reports, regarding the putative role of gut microbiota dysbiosis-induced cardiovascular diseases”

Insect microbiome

Cellulolytic activity and structure of symbiotic bacteria in locust guts – L-J Su – Genetics and Molecular Research

“The diversity of gut symbiotic bacteria was studied using denaturing gradient gel electrophoresis (DGGE). “

Soil microbiome

Effects of Manure Compost Application on Soil Microbial Community Diversity and Soil Microenvironments in a Temperate Cropland in China – Zhen Zhen – PLOS ONE

“Denaturing gradient electrophoresis (DGGE) fingerprinting analysis showed that the structure and composition of bacterial and fungi communities in the six fertilizer treatments varied at different levels. “

Water microbiome

Substratum-Associated Microbiota – Furey, Paula C.; Liess, Antonia – Water Environment Research

“In this review of the 2013 literature, advances in laboratory, field, and assessment methods are highlighted as are updates in taxonomy and systematics.”

More microbiology

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

Donia et al. have carried out the first systematic screen of biosynthetic gene clusters (BGCs) in the healthy human microbiota and found that BGCs for the thiopeptide class of antibiotics are widely distributed.”

First aid kit for cholera – Andrea Du Toit – Nature Reviews Microbiology

“In a new study, Gordon and colleagues examined the role of the human gut microbiota in V. cholerae infection and showed that one of its members, Ruminococcus obeum, decreases the expression of V. cholerae virulence factors to limit colonization.”

Microbes in the news

* A Poop Bank in Massachusetts Will Pay You $40 Every Day – Chelsea Rice – Boston.com

“All you have to do is visit OpenBiome, launched in 2012 as the only independent nonprofit stool bank in the country.”

Study reveals rats in NYC carry variety of infectious bacteria – Larry McShane – New York Daily News

“The first-of-its-kind study showed the rodents carrying an average of two bacteria capable of causing gastrointestinal problems for humans and the Seoul hantavirus, which causes a potentially life-threatening fever and kidney failure.”

* New Genes = New Archaea? – Molly Sharlach – The Scientist

“The study, published today (October 15) in Nature, also suggests that genetic transfers from bacteria to archaea are at least five times more common than from archaea to bacteria.”

Bik’s Picks

“Epicenters” of resilience – Mary Lou Zoback – Science

“The 25th anniversary of the magnitude (M) 6.9 Loma Prieta earthquake that struck the San Francisco Bay Area on 17 October 1989 is a fitting time to examine what progress has been made in increasing community resilience to minimize seismic risk. “

Cells’ powerhouses were once energy parasites: Study upends current theories of how mitochondria began – Science Daily

“Parasitic bacteria were the first cousins of the mitochondria that power cells in animals and plants — and first acted as energy parasites in those cells before becoming beneficial, according to a new study”

How Did We Become a Society Suspicious of Science? – Keith M. Parsons – Huffington Post

“But something has been lost. Fifty years ago science was king. Science had respect; it was bigger than ideology. No longer. “

 

Biology Week: Bio-bodies Bake Off Public Vote – Physiological Society

“In the lead up to biology week we set you a challenge! We wanted you to celebrate the science of life by creating your own physiology bakes, and you didn’t let us down! ”

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Non-human microbiome digest, October 14, 2014

Diatoms in aquatic animals, bacteria in agaves and soybeans, and bacteria in artificial soil.

Animal microbiome

Diatoms in cytologic specimens of aquatic animals – Part I, fecal samples – Nicole StacyDiatoms in cytologic specimens of aquatic animals – Part II, dermal, respiratory, and gastric samples – Nicole Stacy – Veterinary Clinical Pathology

“Diatoms are a common finding in cytologic samples of aquatic animals…and it is necessary to differentiate these microbiota from parasite ova or protozoa.”

Impacts of large-bodied crustaceans on the microbial loop – Krystyna Kalinowska – Hydrobiologia

“Three alien crustacean species (Daphnia pulex, Simocephalus vetulus and Macrocyclops albidus) were collected from the regional species pool and added to mesocosms that were filled with water from a eutrophic lake “

Bacterial Community Composition of Three Candidate Insect Vectors of Palm Phytoplasma (Texas Phoenix Palm Decline and Lethal Yellowing) –  Christopher M. Powell – Current Microbiology

“Individuals from each species were subjected to 16S bacterial community sequencing using the Roche 454 platform, providing new information regarding the previously unexplored bacterial communities present in putative vectors.”

Plant microbiome

Diazotrophic potential among bacterial communities associated with wild and cultivated agaves – Damaris Desgarennes – FEMS Microbiology Ecology

“Here, we investigated the bacterial communities associated with two Agave species by 16S rRNA-DGGE fingerprinting and sequencing.”

Spatio temporal influence of isoflavonoids on bacterial diversity in the soybean rhizosphere – Laura J White – Molecular Plant-Microbe Interactions

“We silenced the biosynthesis of isoflavonoids, a major component of soybean rhizodeposits, using RNA interference in hairy root composite plants, and examined changes in rhizosphere bacteriome diversity.”

Soil microbiome

Artificial soil studies reveal domain-specific preferences of microorganisms for the colonisation of different soil minerals and particles size fractions – Michael Hemkemeyer – FEMS Microbiology Ecology

“this study demonstrates that the mineral composition and the particle size fractions have specific and different selective effects on the three domains”

Improving soil bacterial taxa–area relationships assessment using DNA meta-barcoding – S Terrat – Heredity

“Our objectives in this study were to compare DNA fingerprinting and meta-barcoding approaches for evaluating soil bacterial TAR and the determinism of soil bacterial community assembly on a broad scale. “

The role of stochasticity differs in the assembly of soil- and root-associated fungal communities – Sarah Beck – Soil Biology and Biochemistry

“The importance of spatial and environmental factors in shaping fungal beta diversity was determined over a 500 km transect.”

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Non-human microbiome digest, October 2, 2014

Microbiomes of mares with colic, corals and ascidians, bacteria in plant seeds, ciprofloxacin in compost, and yeast in Turkish sausages.

Mammal microbiome

Diversity and Community Composition of Methanogenic Archaea in the Rumen of Scottish Upland Sheep Assessed by Different Methods – Timothy J. Snelling – PLOS ONE

“Sequences mapping to rumen 16S rRNA and mcrA gene references were extracted from Illumina metagenome data.“

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

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

Changes in the faecal microbiota of mares precede the development of postpartum colic
J. S. Weese – Equine Veterinary Journal

“Next generation sequencing of the V4 region of the 16S rRNA gene was performed on samples from 13 mares that developed colic, 13 mares that did not display colic, and 5 non-pregnant controls.”

Bird microbiome

Correlations between changes in intestinal microbiota composition and performance parameters in broiler chickens – L. A. Rubio – Journal of Animal Physiology and Animal Nutrition

“The composition of the intestinal microbiota was analysed by qPCR at different points of the intestinal tract, and a number of nutritional parameters were also determined.”

Insect microbiomes

Differential Genome Evolution Between Companion Symbionts in an Insect-Bacterial Symbiosis – Gordon M. Bennett – mBio

“To understand how symbiont genome degeneration proceeds, we compared the genomes of symbionts in two leafhopper species”

Metagenome-Wide Association of Microbial Determinants of Host Phenotype in Drosophila melanogaster – John M. Chaston – mBio

“.. we measured two microbiota-responsive host traits, development time and triglyceride (TAG) content, in Drosophila melanogaster flies monoassociated with each of 41 bacterial strains.”

Invertebrate microbiome

Quorum Sensing Signal Production and Microbial Interactions in a Polymicrobial Disease of Corals and the Coral Surface Mucopolysaccharide Layer – Beth L. Zimmer – PLOS ONE

“These findings demonstrate for the first time that AHLs are present in an active coral disease.”

The secret to a successful relationship: lasting chemistry between ascidians and their symbiotic bacteria – Eric W. Schmidt – Invertebrate Biology

Plant microbiome

Plants prepackage beneficial microbes in their seeds – Phys.org

“The researchers, from the University of Notre Dame, presented their findings today at the 5th ASM Conference on Beneficial Microbes.”

Cave microbiome

* Mycobiome of the Bat White Nose Syndrome Affected Caves and Mines Reveals Diversity of Fungi and Local Adaptation by the Fungal Pathogen Pseudogymnoascus (Geomyces) destructans – Tao Zhang – PLOS ONE

“This study was conducted in 2010–2011 in New York and Vermont using 90 samples from four mines and two caves situated within the epicenter of WNS. “

Soil and sediment microbiome

Differential distribution and abundance of diazotrophic bacterial communities across different soil niches using a gene-targeted clone library approach – Basit Yousuf – FEMS Microbiology Letters

“Differential occurrence of diazotrophs was studied by the nifH gene-targeted clone library approach.”

Spatiotemporal Analysis of Bacterial Diversity in Sediments of Sundarbans Using Parallel 16S rRNA Gene Tag Sequencing – Pijush Basak – Microbial Ecology

“The total sediment DNA was extracted and subjected to the 16S rRNA gene pyrosequencing, which resulted in 117 Mbp of data from three experimental stations. “

Ciprofloxacin residues in municipal biosolids compost do not selectively enrich populations of resistant bacteria – Caitlin P. Youngquist – Applied and Environmental Microbiology

“Regression analysis showed that growth of the susceptible strain of E. coli can be reduced given a sufficiently high concentration of ciprofloxacin (P<0.007), a result that is consistent with adsorption being the primary mechanism of sequestration. “

Biogeographic patterns in below-ground diversity in New York City’s Central Park are similar to those observed globally – Kelly S. Ramirez – Proceedings of the Royal Society B

“Here, we present an assessment of soil biodiversity and biogeographic patterns across Central Park in New York City that spanned all three domains of life, demonstrating that even an urban, managed system harbours large amounts of undescribed soil biodiversity.”

Water microbiome

Abundance and Dynamics of Antibiotic Resistance Genes and Integrons in Lake Sediment Microcosms – Björn Berglund – PLOS ONE

“Resistance genes sulI and ermB were quantified in the microcosm sediments with mean abundances 5 and 15 gene copies/106 16S rRNA gene copies, respectively. “

Microbial composition of the activated sludge of Moscow wastewater treatment plants
A. Yu. Kallistova – Microbiology

“FISH investigation revealed that aerobic sludge were eubacterial communities; the metabolically active archaea contributed insignificantly.”

Phytoplankton, bacterioplankton and virioplankton structure and function across the southern Great Barrier Reef shelf – Daniel M. Alongi – Journal of Marine Systems

“Phytoplankton, bacteria and virus dynamics are driven by across-shelf changes in water chemistry and hydrography.”

Food microbiology

Pulque production from fermented agave sap as a dietary supplement in Prehispanic Mesoamerica – Marisol Correa-Ascencio – PNAS

“A novel bacterial lipid biomarker approach is reported, which provides a new means of documenting the consumption of bacterially fermented alcoholic beverages in antiquity worldwide.”

Biodiversity of Yeast Mycobiota in “Sucuk,” a Traditional Turkish Fermented Dry Sausage: Phenotypic and Genotypic Identification, Functional and Technological Properties – Ismet Ozturk, and Osman Sagdic – Journal of Food Science

“The yeast isolates were determined as genotypic using 2 different polymerase chain reaction (PCR) methods (rep-PCR and RAPD-PCR).”

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Animal microbiome digest, September 16, 2014

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

Mammal microbiome

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

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

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

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

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

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

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

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

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

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

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

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

Insect microbiome

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

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

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

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

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

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

Invertebrate microbiome

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

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

Plant microbiome

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

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

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

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

Soil microbiome

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

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

Water microbiome

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

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

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

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

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

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

Built environment microbiome

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

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

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

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

Food microbiology

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

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

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

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

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

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

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Microbiome digest, August 27, 2014

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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Non-human microbiome, August 25, 2014

Microbiotas of pigs, two fish species in the same pond, coral-algal associations, hypersaline soil, and marine eukaryotes.

Mammal microbiome

The influence of host’s genetics on the gut microbiota composition in pigs and its links with immunity traits – J. Estellé – Proceedings, 10th World Congress of Genetics Applied to Livestock Production

“A cohort of 60-days old piglets was assessed for fecal microbiota composition by pyrosequencing of the 16S rDNA. “

Fish microbiome

* Do the intestinal microbiotas differ between paddlefish (Polyodon spathala) and bighead carp (Aristichthys nobilis) reared in the same pond? – Xuemei Li – Journal of Applied Microbiology

“After 30-days of rearing the intestinal microbiota of the two fish species were assessed by pyrosequencing of 16S rRNA genes”

Insect microbiome

Microbial Associates of the Vine Mealybug Planococcus ficus (Hemiptera: Pseudococcidae) under Different Rearing Conditions – Lilach Iasur-Kruh – Microbial Ecology

“To examine the possible role of microbial symbionts in virus transmission, the archaeal, bacterial, and fungal microbiota of field and laboratory P. ficus were characterized using molecular and classical microbiological methods. “

Coral microbiome

* The extended phenotypes of marine symbioses: ecological and evolutionary consequences of intraspecific genetic diversity in coral–algal associations – John E. Parkinson and Iliana B. Baums – Frontiers in Microbiology

“Here, we hypothesize that unique combinations of coral and algal individuals yield functional diversity that affects not only the ecology and evolution of the coral holobiont, but associated communities as well. “

Soil microbiome

Salinity-induced differences in soil microbial communities around the hypersaline Lake Urmia – Mohsen Barin – Soil Research

“We tested the hypotheses that salinity reduces microbial biomasses and change the structure of the microbial community.”

Water microbiome

Microbial Community Response to Chlorine Conversion in a Chloraminated Drinking Water Distribution System – Hong Wang – Environmental Science & Technology

“Although high throughput sequencing of 16S rRNA genes revealed a distinct community shift and higher diversity index during the chlorine burn, it steadily returned towards a condition more similar to pre-burn than burn stage.”

Metagenetic analysis of patterns of distribution and diversity of marine meiobenthic eukaryotes – Vera G. Fonseca – Global Ecology and Biogeography

“Here, we ask: (1) if the macroecology of meiobenthic communities is explained mainly by dispersal constraints or by environmental conditions; and (2) if levels of meiofaunal diversity surpass existing estimates based on morphological taxonomy.”

Microbiology of the Built Environment

* A disturbing trend – casual and reckless use of antimicrobial agents in building materials – Jonathan Eisen – MicroBEnet

“So they put in flooring that apparently was impregnated with some sort of antibacterial agent and they have no evidence that it works. “

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