October 11, 2019

Good morning everyone!

Today’s digest is full of great reviews paper, among else- from the gut microbiome to bacterial metabolic modelling. Also featured is a lovely paper regarding vaginal microbiome transplantation (with interesting translational meaning!) and a food-for-thought paper about microbiology past, present and furture (1st in the list down).

Have a great weekend and happy Jewish New year!

Food for Thought

Shift in the paradigm towards next-generation microbiology, Blaz Sterz & Luka Kronegger, FEMS Microbiology Letters

Human microbiome

** Re‐assessing microbiomes in the low‐biomass reproductive niche, Jessica L. O’Callaghan, BJOG

** Incorporating functional trade-offs into studies of the gut microbiota, Aspen T Reese, Curr. Opi. Microbiology

** Gut microbial metabolites in depression: understanding the biochemical mechanisms, Giorigia Caspani, microbial cell

** Vaginal microbiome transplantation in women with intractable bacterial vaginosis, Ahinoam Lev-Sagie, Nature Medicine

Gut microbiome diversity is associated with sleep physiology in humans, Robert P. Smith, PLOS One

Microbial Interactions in Oral Communities Mediate Emergent Biofilm Properties, P.I. Diaz, J. Dental Research

Animal microbiome

A wild microbiome improves mouse modeling of the human immune response, Sara E. Hamiltion, Lab Animal

Gut Microbiota of Migrating Wild Rabbit Fish (Siganus guttatus) Larvae Have Low Spatial and Temporal Variability, Duy Le, Microbial Ecology

Environmental microbiome

** Implications of indoor microbial ecology and evolution on antibiotic resistance, Sarah Ben Maamar, J. Exp. science & Env. Epid.

A microcosm approach highlights the response of soil mineral weathering bacterial communities to an increase of K and Mg availability, O. Nicolitch, Scientific Reports

Preceding crop and tillage system affect winter survival of wheat and the fungal communities on young wheat roots and in soil, Hanna Friberg, FEMS Microbiology Letters

Viral microbiome

A review on viral metagenomics in extreme environments, Sonia Davila-Ramos, Frontiers in Microbiology

Methods in microbiology

Multi-faceted approaches to discovering and predicting microbial nutritional interactions, Sebastian Gude, Curr. Opi. Biotechnology

Artificial neural network-assisted Fourier transform infrared spectroscopy for differentiation of Salmonella serogroups and its application on epidemiological tracing of Salmonella Bovismorbificans outbreak isolates from fresh sprouts, Helene Obereuter, FEMS Microbioogy Letters

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

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 26,2019

Good morning/afternoon wherever you are!

Today’s digest is really focusing on the environment- cilmate change (check the section right below), water, stone and coral reefs. We also included two microbiome framework papers worth reading and for all the athelates (and does who struggle to go the gym)- How is our microbiome linked to physical performance?

Have a good one!

Microbiology and Climate Change

The Microbiologists’ Warning–  Consensus Statement proclaiming that microorganisms are so critical to achieving an environmentally sustainable future that ignoring them risks the fate of Humanity. Please enter the link for more details and getting involved.

Scientists’ warning to humanity: microorganisms and climate change, Riccardo Cavicchioli, Nature Microbiology

Microbiome framework and methods

Combining Molecular Observations and Microbial Ecosystem Modeling: A Practical Guide, Ferdi L. Hellweger, Ann. Rev. Marine Science

Establishing microbial composition measurement standards with reference frames, James T. Morton, Nature Communications

Mining traits for the enrichment and isolation of not-yet-cultured populations, An-Ni Zhang, Microbiome

Human and animals microbiome

Meta-omics analysis of elite athletes identifies a performance-enhancing microbe that functions via lactate metabolism, Jonathan Scheiman, Nature Medicine

Impact of different hypercaloric diets on obesity features in rats: a metagenomics and metabolomics integrative approach, Andreu Gual-Grau, J. Nutritional Biochemistry

*Method: A Guide for Ex Vivo Handling and Storage of Stool Samples Intended for Fecal Microbiota Transplantation, Sebestian D. Burz, Scientific Reports

Skin microbiome modulation induced by probiotic solutions, Bernhard Paetzhold, Microbiome

Environmental microbiome

Microbial dynamics of biosand filters and contributions of the microbial food web to effective treatment of wastewater-impacted water sources, Tara M. Webster, AEM

Elucidating the ecological networks in stone‐dwelling microbiomes, Moussa Louati, Environmental Microbiology

Microbial indicators of environmental perturbations in coral reef ecosystems, Betina Glasl, Microbiome

The Role of the Human Microbiome in Chemical Toxicity, Jason M. Koontz, Int. j. Toxicology

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

May 14, 2019

Good morning microbe lovers! This digest presents papers for everyone taste, plus some really nice general microbiology and science papers. Check out cool snow algae microbiome in Antarctica, soil aggregates microbiome, DNA extraction methods in studying animal microbiomes and more.

Don’t forget to spread MD with friends, colleges and others- it really helps us knowing our hard work is actually being read.

General microbiology

Into the wild: microbiome transplant studies need broader ecological reality , Christopher J. Greyson-Gaito, EcoEcoRxiv

Predicting the decision making chemicals used for bacterial growth, Kazuha Ashino, Scientific Reports

A longitudinal big data approach for precision health, Sophia Miryam Schussler-Fiorenza Rose, Nature Medicine

Human Microbiome

Mammographic breast density and its association with urinary estrogens and the fecal microbiota in postmenopausal women, Gieira S. Jones, PLOS One

Periodontal Health and Oral Microbiota in Patients with Rheumatoid Arthritis, K. Erikkson, Journal of Clinical Medicine

Animal Microbiome

Habitat fragmentation is associated with dietary shifts and microbiota variability in common vampire bats, Melissa R. Ingala, Ecology and Evolution

Fungal disease and temperature alter skin microbiome structure in an experimental salamander system, CR Muletz-Wolz, Molecular Ecology

Variations of the intestinal gut microbiota of farmed rainbow trout, Oncorhynchus mykiss (Walbaum), depending on the infection status of the fish, A.N Parshukov, Journal of Applied Microbiology

Responses of microbial community structure in turbot (Scophthalmus maximus) larval intestine to the regulation of probiotic introduced through live feed, Yan Jiang, PLOS One

Assessment of microbial communities on freshly killed wild boar meat by MALDI-TOF MS and 16S rRNA amplicon sequencing, M.F. Peruzy, Int. Food Microbiology

**Methods Impact of DNA extraction methods on the observed microbial communities from the intestinal flora of the penaeid shrimp Litopenaeus vannamei, Boyun Jiang, FEMS Microbiology Letters

Air Microbiome

** Snow algae communities in Antarctica: metabolic and taxonomic composition, Matthew P. Davey, The New Phytologist

Soil and Plants Microbiome

**Minireview Soil aggregate microbial communities: Towards understanding microbiome interactions at biologically relevant scales, Regina L. Wilpiszeski, App. Env. Microbiology

Comparative microbiome analysis of two different long-term pesticide contaminated soils revealed the anthropogenic influence on functional potential of microbial communities, Raj Kumar Regar, Science of the Total Environment

Interpreting distance‐decay pattern of soil bacteria via quantifying the assembly processes at multiple spatial scales, Maomao Feng, MicrobiologyOpen

Complex microbial communities drive iron and sulfur cycling in Arctic fjord sediments, J. Buongiorno, App. Env. Microbiology

Defining the root endosphere and rhizosphere microbiomes from the World Olive Germplasm Collection, Antonio Jose Fernandez-Gonzales, bioRxiv

Microbiome in the news

Human gut microbiome physiology can now be studied in vitro using Organ Chip technology, Phys.org

Inspirotec Inc and Argonne National Laboratory Collaborate on Largest Study to Date of Airborne Allergens and Microbiome in Same Homes, Globenewswire

April 25, 2019

Good morning everyone! (and apologies for the delay, a technical issue regarding the system time difference between Israel and US Pacific time :)).

Due to yesterday extremely rich digest, today’s post will be short- but diverse! Spreading from gut microbiome in infants and beetles, to the effect of microbial communities on sweet wine quality. As a bonus for the upcoming weekend, at the end of the post you’ll find a link to an article listing 10 recommended biotech podcasts.

Happy holidays for all!

General Science and Microbiology

Failure to vaccinate and vaccine failure– Editorial- Nature Microbiology

The problem with unadjusted multiple and sequential statistical testing– Casper Albers- Nature Communications

Human microbiome

**Review – What did we learn from multiple omics studies in asthma?– Olga Ivanova- Allergy

Fecal microbiota transplant for Crohn disease: A study evaluating safety, efficacy, and microbiome profile– Liat Gutin- ueg

Specific class of intrapartum antibiotics relates to maturation of the infant gut microbiota: a prospective cohort study– Modupe O. Coker- BJOG

The Gut Microbiome on a Periodized Low-Protein Diet Is Associated With Improved Metabolic Health– Zhencheng Li- Frontiers in Microbiology

Plant microbiome

Characterization of Rhodopseudomonas palustris population dynamics on tobacco phyllosphere and induction of plant resistance to Tobacco mosaic virus infection– Pin Su- bioRxiv

The plant host induces antibiotic production to select the most beneficial colonizers– Ariel Ogran- AEM

Microbial network and soil properties are changed in bacterial wilt susceptible soil– Gaufo Qi- AEM

Water Microbiomes

Fates of antibiotic resistance genes in a distributed swine wastewater treatment plant– Qing-Bin Yuan- Water Environment Research

** Metabolic potential of uncultured bacteria and archaea associated with petroleum seepage in deep-sea sediments– Xiyang Dong- Nature Communications

Animal microbiome

Gut anatomical properties and microbial functional assembly promote lignocellulose deconstruction and colony subsistence of a wood-feeding beetle– Ceja Navarro- Nature Microbiology

Gut microbiome-derived phenyl sulfate contributes to albuminuria in diabetic kidney disease– Koichi kikuchi- Nature Communications

Honeybee-specific lactic acid bacterial supplements have no effect on American foulbrood infected honeybee colonies– Jorg G. Stephan- AEM

Food microbiome

Influence of microbial communities on the chemical and sensory features of Falanghina sweet passito wines– F De Fillips- Europe PMC

Microbiome in the News

The Asia Pacific human microbiome market is expected to reach US$ 207.81 Mn in 2025 -Cision

**UPDATED- Critical Reading required– Antibiotics: beneficial side effects are starting to come to light– Claire Bourke- The Conversation. I’m bringing about this post in order to encourage a discussion regarding the issues and claims that were written in this non-scientific article. You’re welcome to share your thoughts about it at the comments section below.

Podcasts

Top 10 Biotech Podcasts to Listen to this Spring– Clara Rodriguez Fernandez- Labiotech.eu

**Personal recommendation- This Week in Microbiolgy (TwiM)