13 July, 2019

Good morning everyone!

Today’s digest is kind of diverse (as always), with great papers about women microbiome, sardines gut microbiome, a great review about soil aggregates and, corals microbiomes and much more. Be sure to read the first paper right down here- The Conceptual Ecology of the Human Microbiome. Have a great weekend!

Human microbiome

**From June 2019, but a must-read nonetheless: The Conceptual Ecology of the Human Microbiome, Morar and Bohannan, Q. R. Biology

Interaction between the nasal microbiota and S. pneumoniae in the context of live-attenuated influenza vaccine, Wouter A. A. de Steenhuijsen Piters, Nature Communications

Selected Immunological Mediators and Cervical Microbial Signatures in Women with Chlamydia trachomatis Infection, Simone Filardo, mSystems

Discovery of potential genes contributing to the biosynthesis of short-chain fatty acids and lactate in gut microbiota from systematic investigation in E. coli, Chunhua Zhao, MPMI

Secondary bile acid ursodeoxycholic acid (UDCA) alters weight, the gut microbiota, and the bile acid pool in conventional mice, Jenessa A. Winston, bioRxiv

Microbiota supplementation with Bifidobacterium and Lactobacillus modifies the preterm infant gut microbiota and metabolome, Cristina Alcon-Giner, bioRxiv

Animal microbiome

A Cross-Sectional Study of Compositional and Functional Profiles of Gut Microbiota in Sardinian Centenarians, Lu Wu, mSystems

Contribution of gut microbiota to metabolism of dietary glycine betaine in mice and in vitro colonic fermentation, Ville M. Koistinen, Microbiome

Coral bacterial community structure responds to environmental change in a host-specific manner, Maren Ziegler, Nature Communications

Soil microbiome

**Mini-review: Soil Aggregate Microbial Communities: Towards Understanding Microbiome Interactions at Biologically Relevant Scales, Regina L. Wilpiszeski , AEM

Continuous monoculture shapes root and rhizosphere fungal communities of corn and soybean in soybean cyst nematode-infested soil, Noah Strom, Phytobiomes

Engineered root bacteria release plant-available phosphate from phytate, Christine N. Shulse, AEM

Diversity and Characterization of Oomycetes Associated with Corn Seedlings in Michigan, J. A. Rojas, Phytobiomes

Environmental microbiome

Diverse, abundant and novel viruses infecting “unculturable” but abundant marine bacteria, Zefeng Zhang, bioRxiv

Biocide resistance and transmission of Clostridium difficile spores spiked onto clinical surfaces from an American healthcare facility, Calie Dyer, AEM

Microbiome in the news

Lab Startup uBiome Laying Off About Half of Global Workforce

Microbiome Repairing Food for Malnourished Children Beats Current Therapy

June 13, 2019

Good morning everyone!

Today the focus is almost entirely on environmental microbiology- plant, soil and water habitats. Check also the methods paper regarding activating silent BGCs (a true challenge for drug discovery).

General Microbiology

A multiphase theory for spreading microbial swarms and films, Siddarth Srinivasan, eLIFE

Methods

Advances in microbial culturing conditions to activate silent biosynthetic gene clusters for novel metabolite production, Hailey A. Tomm, J. Industrial Microbiology % Biotechnology

A set of modular and integrative vectors for synthetic biology in Streptomyces, Celine Aubry, AEM

Revealing microbial assemblage structure in the human gut microbiome using latent Dirichlet allocation, Shion Hosoda, bioRxiv

Animal microbiome

The Insect Virome: Opportunities and Challenges, BC Bonning, Curr. Issues Mol Bio.

Host species and site of collection shape the microbiota of Rift Valley fever vectors in Kenya, David P. Tchouassi, PLOS Neglected Tropical Diseases

Microbiomes of stony and soft deep-sea corals share rare core bacteria, Christina A. Kellogg, Microbiome

Plant Microbiome

Identification and Characterization of the Core Rice Seed Microbiome, Alexander W. Eyre, Phytobiome

Microbiota Associated with Sclerotia of Soilborne Fungal Pathogens – A Novel Source of Biocontrol Agents Producing Bioactive Volatiles, Pascal Mulner, Phytobiome

ffects of agricultural management on rhizosphere microbial structure and function in processing tomato, Jennifer E. Schmidt, AEM

Environmental microbiome

Methylotrophs and Methylotroph Populations for Chloromethane Degradation, F Bringel, Curr Issues Mol Bio.

Diversity of Methane Cycling Microorganisms in Soils and Their Relation to Oxygen, C Knief, Curr Issues Mol Bio.

Microbiomes in Ground Water and Alternative Irrigation Water, and Spinach Microbiomes Impacted by Irrigation with Different Types of Water, Ganyu Gu, Phytobiome

E

Microbiome in the market

Macrogen Announces Strategic Investment in Australian Microbiome Company, Microba

New DuPont research pact has animal microbiome focus

Microbiome digest, October 21, 2014

Human oral microbiome

Abstract 4834: Microbiome in Oral Epithelial Dysplasia and Squamous Cell Carcinoma
Deepak Saxena – Cancer Research

“PCR amplicons targeting V3-V5 region of 16S rRNA gene were sequenced by 454 pyrosequencing. “

Human respiratory microbiome

Microbial Communities in the Upper Respiratory Tract of Patients with Asthma and Chronic Obstructive Pulmonary Disease – HeeKuk Park – PLOS ONE

“To account for the qualitative and quantitative diversity of the 16S rRNA gene in the oropharynx, the microbiomes of 18 asthma patients, 17 COPD patients, and 12 normal individuals were assessed using a high-throughput next-generation sequencing analysis.”

Human gut microbiome

Decreased bacterial diversity characterizes an altered gut microbiota in psoriatic arthritis and resembles dysbiosis of inflammatory bowel disease – Jose U. Scher – Arthritis & Rheumatology

“High-throughput 16S rRNA pyrosequencing was utilized to compare community composition of gut microbiota in PsA patients, subjects with psoriasis of the skin and healthy, matched-controls. “

Pregnancy and birth

The Salivary Scavenger and Agglutinin in Early Life: Diverse Roles in Amniotic Fluid and in the Infant Intestine – Martin Parnov Reichhardt – Journal of Immunology

“The present study revealed that SALSA was present in the amniotic fluid (AF) and exceptionally enriched in both meconium and feces of infants. “

Animal microbiome

* Unique and shared responses of the gut microbiota to prolonged fasting: a comparative study across five classes of vertebrate hosts – Kevin D. Kohl – FEMS Microbiology Ecology

“We used 16S rRNA sequencing to document changes in colonic and cecal microbiomes of animals representing five classes of vertebrates at four time points through prolonged fasting: tilapia, toads, geckos, quail, and mice. “

GeoChip-based insights into the microbial functional gene repertoire of marine sponges (HMA, LMA) and seawater – Kristina Bayer – FEMS Microbiology Ecology

“By use of GeoChip, altogether 20,273 probes encoding for 627 functional genes and representing 16 gene categories were identified”

Natural volcanic CO2 seeps reveal future trajectories for host–microbial associations in corals and sponges – Kathleen M Morrow – ISME Journal

“The corals Acropora millepora and Porites cylindrica were less abundant and hosted significantly different microbial communities at the CO2 seep than at nearby control sites <500 m away.”
Plant microbiome

Phylogenetic conservatism in plant-soil feedback and its implications for plant abundance – Brian L. Anacke – Ecology Letters

“We conclude that soil biota influence the abundance of close plant relatives in nature.”

Bioreactor microbiome

Influence of Acidic pH on Hydrogen and Acetate Production by an Electrosynthetic Microbiome – Edward V. LaBelle – PLOS ONE

“Production of hydrogen and organic compounds by an electrosynthetic microbiome using electrodes and carbon dioxide as sole electron donor and carbon source, respectively, was examined after exposure to acidic pH (~5). “

Metagenomics / Transcriptomics / Bioinformatics

Census-based rapid and accurate metagenome taxonomic profiling – Amirhossein Shamsaddini – BMC Genomics

“We have developed a robust subsampling-based algorithm implemented in a tool called CensuScope meant to take a ‘sneak peak’ into the population distribution and estimate taxonomic composition as if a census was taken of the metagenomic landscape. “

Metatranscriptomes from diverse microbial communities: assessment of data reduction techniques for rigorous annotation – Andrew Toseland – BMC Genomics

“To investigate the effect of such techniques on the annotation of metatranscriptome data we assess two commonly employed methods: clustering and de-novo assembly. To do this, we also developed an approach to simulate 454 and Illumina metatranscriptome data sets with varying degrees of taxonomic diversity. “

Microbial Ecology

Mathematical Modeling of Microbial Community Dynamics: A Methodological Review – Hyun-Seob Song – Processes

“In this article, we provide an overview of mathematical tools that include not only current mainstream approaches, but also less traditional approaches that, in our opinion, can be potentially useful. “

A phylogenetic perspective on species diversity, β-diversity, and biogeography for the microbial world – Albert Barberán† and Emilio O. Casamayor – Molecular Ecology

“We explored links between evolution/phylogeny and community ecology using bacterial 16S rRNA gene information from a high altitude lakes district dataset to describe phylogenetic community composition, spatial distribution, and β-diversity and biogeographical patterns applying evolutionary relatedness without relying on any particular operational taxonomic unit definition.”

Distance-Decay and Taxa-Area Relationships for Bacteria, Archaea and Methanogenic Archaea in a Tropical Lake Sediment – Davi Pedroni Barreto – PLOS ONE

“The samples were analyzed using T-RFLP (Terminal restriction fragment length polymorphism) targeting mcrA (coding for a subunit of methyl-coenzyme M reductase) and the genes of Archaeal and Bacterial 16S rRNA.”

More microbiology

From Denise Monack’s lab: Role of disease-associated tolerance in infectious superspreaders – Smita Gopinath – PNAS USA

“Using a mouse model of Salmonella infection, we show that levels of Salmonella are equivalent between antibiotic-treated superspreader and nonsuperspreader hosts; however, superspreader hosts are uniquely able to tolerate antibiotic treatment, unlike nonsuperspreader hosts. “

*Also see:  Antibiotics may help Salmonella spread in infected animals, scientists learn – Stanford Medicine News

Spatial organization of bacterial chromosomes – Xindan Wang, David Z Rudner – Current Opinion in Microbiology

“Here, we summarize these different patterns highlighting similarities and differences and discuss the protein factors that help establish and maintain them.”

Bacterial healers: Microbes can redeem themselves to fight disease – Susan Gaidos – Science News

“It’s just a matter of time before bacterial-based treatments become a routine part of a doctor’s toolkit, says microbiologist Robert Britton of the Baylor College of Medicine in Houston, who is studying the relationship between microbes and human health. “

Techniques

Rapid fingerprinting of methanogenic communities by high-resolution melting analysis – Jaai Kim, Changsoo Lee – Bioresource Technology

“The new method produced robust community clustering and ordination results comparable to the results from the commonly used denaturing gradient gel electrophoresis (DGGE) performed in parallel.”

Microbes in the news

Our unique ‘microbial aura’ travels with us wherever we go – Science Friday – PRI

“Unless you lived exactly the same life as me, you would not have the same microbiome. You are, in essence, microbially unique,” explains Jack Gilbert

We’re making a Microbiome Documentary Series and could use your Help – Jamie – Reddit

“My name’s Jamie and I’m part of a team trying to crowdfund a documentary series on the human microbiome titled: ‘Redefining Human’.”

Building houses with bacteria – Euronews

“Houses of the future could be partially built with bacteria. It sounds like science fiction but researchers involved in an EU-backed project in Madrid are working towards making this a concrete reality.”

Bik’s Picks

The Role of Surface Chemistry in Adhesion and Wetting of Gecko Toe Pads – Ila Badge – Scientific Reports

“As expected, under wet conditions, adhesion on a hydrophilic surface (glass) was lower than that on a hydrophobic surface (alkyl-silane monolayer on glass).”

Scientists prepare for an 8-month mission to Mars – on Earth soil- BetaWired

“There’s a new experiment commencing in Hawaii, and the results will help NASA better prepare its astronauts for a lengthy mission to Mars.”

White rhino subspecies is down to one breeding male – Andrea James – BoingBoing

“Sad news from Kenya: the northern white rhino subspecies is down to one breeding male with the death of Suni this month. Only six remain.”

Scientists restore hearing in noise-deafened mice, pointing way to new therapies – ScienceDirect

“Scientists have restored the hearing of mice partly deafened by noise, using advanced tools to boost the production of a key protein in their ears.”

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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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Microbiome digest, August 21, 2014

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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