April 7, 2020

Hi everyone! This is my first contribution to the daily digest, and I’ll follow others’ lead by starting with the latest preprints concerning Covid-19. Away from the ongoing pandemic, some of the highlights include a look at how commensal gut microbes interact with pathogens, and an insight into deep sea oceanic crust microbiomes.

It seems to be a relatively quiet day today, so I’ve included an article from the University of Bristol which looks at how nanoscopic pillars on the surface of some insect wings protect them against bacteria. Perhaps only loosely a microbiome paper, but it’s worth a read for its electron microscopy alone!

COVID-19

Structure of the SARS-CoV-2 spike receptor-binding domain bound to the ACE2 receptor – Lan et al. – Nature

Preprint: Atazanavir inhibits SARS-CoV-2 replication and pro-inflammatory cytokine production – Fintelman-Rodrigues et al.

Preprint: Amantadine disrupts lysosomal gene expression; potential therapy for COVID19 – Smieszek et al.

Preprint: Potent Antiviral Activities of Type I Interferons to SARS-CoV-2 Infection – Mantlo et al.

Human gut microbiome

Dissecting individual pathogen-commensal interactions within a complex gut microbiota community – Hassall and Unnikrishnan

Animal microbiome

Antibacterial effects of nanopillar surfaces are mediated by cell impedance, penetration and induction of oxidative stress – Jenkins et al. – Nature Communications

Water and extremophile microbiome

Deep microbial proliferation at the basalt interface in 33.5–104 million-year-old oceanic crust – Suzuki et al.Communications Biology

Food microbiology

How does the microbiome impact pig health? – Sarah Mikesell – The Pig Site

Microbes in the news

Lifestyle trumps geography in determining makeup of gut microbiomeEurekAlert!

Microbes on the market

Gilead taps Second Genome for microbiome biomarker help in a potential $1.5B deal – Connor Hale – FierceBiotech.com

March 13, 2020

Good moring y’all!

Today’s digest is relatively short, but rather diverse- from the potential characteristics of scientific tweets readers, through cancer microbiome and horses fecal transplants, as well as endophytes microbiomes in different biomes and plants. Also, if you’re still unfaimilar with the ‘Talking about Biotech’ podcast (by Kevin Folta), I highly recommend to add it to your list. The latest episode talks, of course, about the Corona outbreak, and if you’ll go a bit earlier you will find plenty interesring and insightful episodes.

And lastly- pls stay safe! in Israel, as in other parts of the world, conferences are being cancelled, group meetings are rescheduled and we were highly encouraged to work from home (go bioinformatics!). Remember- there is not a single experiment that is more important than your and your love ones health.

General microbiology

Quantifying and contextualizing the impact of bioRxiv preprints through social media audience segmentation, Jedidiah Carlson , bioRxiv

An optimised saliva collection method to produce high-yield, high-quality RNA for translational research, Roisin Sullivan, PLOS ONE

The Vibrio cholerae Type VI Secretion System: Toxins, Regulators and Consequences, Cristian V. Crisan, Env. Micro.

Human microbiome

Microbiome analyses of blood and tissues suggest cancer diagnostic approach, Gregory D. Poore , Nature

Changes in key vaginal bacteria among postpartum African women initiating intramuscular depot-medroxyprogesterone acetate, Bridget M. Whitney ,PLOS ONE

Animal microbiome

The fecal microbiota of healthy donor horses and geriatric recipients undergoing fecal microbial transplantation for the treatment of diarrhea, Caroline A. McKinney , PLOS ONE

Low mutational load and high mutation rate variation in gut commensal bacteria, Ricardo S. Ramiro, PLOS Biology

Marine microbiome

Diel, daily, and spatial variation of coral reef seawater microbial communities, Laura Weber , PLOS ONE

Short‐term changes in polysaccharide utilization mechanisms of marine bacterioplankton during a spring phytoplankton bloom, Greta Reintjes, Env. Micro.

Plant and Soil microbiome

The diversity and distribution of endophytes across biomes, plant phylogeny, and host tissues—how far have we come and where do we go from here?, Joshua G. Garrison, Env. Micro.

Tissue age, orchard location and disease management influence the composition of fungal and bacterial communities present on the bark of apple trees, Elena Arrigoni , Env. Micro.

Salmonella persistence in soil depends on reciprocal interactions with indigenous microorganisms, Jasper Schierstaedt , Env. Micro.

Bioinformatics

Random sampling in metagenomic sequencing leads to overestimated spatial scaling of microbial diversity, Qichao Tu , Env. Micro.

February 28, 2020

Good morning/afternoon y’all! today’s digest features some interesting-to-read genral biotech and ecology papers, as weel as the first gene catalouge of the vaginal microbiome, American pets microbiome revealed, cool microbiome engineering for biocontrol purpose in agriculture, a bunch of salt- and sweet-water microbiome studies and more!

Have a great weekend! put the guilt aside and enjoy some time with your spouse, family, pets, hobbies and anything else that you enjoy!

General Science

is is a very cool paper, beuatifuly presenting the connection and applicatino of two very ‘hot’ topics in today biotechnology world- AI and drug discovery:A Deep Learning Approach to Antibiotic Discovery- A Deep Learning Approach to Antibiotic Discovery, Jonathan M. Stokes, Cell

** Novel Outlook in Microbial Ecology: Nonmutualistic Interspecies Electron Transfer, Roman Moscoviz, Trends in Microbiology

A solution to minimum sample size for regressions, David J. Jenkins , PLOS One

The relationship between the host genome, microbiome, and host phenotype, Harald Brussow, Env. Micro.

Human microbiome

** A comprehensive non-redundant gene catalog reveals extensive within-community intraspecies diversity in the human vagina, Bing Ma, Nature Communications

Gut microbiota plasticity is correlated with sustained weight loss on a low-carb or low-fat dietary intervention, Jessica A. Grembi, Sci. Rep.

Analysis of healthy reference ranges for clinically relevant gut microbial indicators: A large web-based cohort study in Japan, Satoshi Watanabe , bioRxiv

Short chain fatty acids produced by colonizing intestinal commensal bacterial interaction with expressed breast milk are anti-inflammatory in human immature enterocytes, Nan Zheng, PLOS One

Animal microbiome

Characterization of gut microbiomes of household pets in the United States using a direct-to-consumer approach, Aashish R. Jha, PLOS One

Repeated sleep disruption in mice leads to persistent shifts in the fecal microbiome and metabolome, Samuel J. Bowers, PLOS One

Insect microbiome

**Engineering bacterial symbionts of nematodes improves biocontrol potential of the western corn rootworm, Ricardo A. R. Machado, Nature Biotechnology

Plant and soil microbiome

Genome wide association study reveals plant loci controlling heritability of the rhizosphere microbiome, Siwen Deng , bioRxiv

Differentiation strategies of soil rare and abundant microbial taxa in response to changing climatic regimes, Yuting Liang , Env. Micro.

Network analysis infers the wilt pathogen invasion associated with non-detrimental bacteria, Qiolong Hu , npj biofims and microbiomes

Marine microbiome

Exploring the resistome, virulome and microbiome of drinking water in environmental and clinical settings, Marcela Franca Dias, Water Research

Niche partitioning of methane-oxidizing bacteria along the oxygen–methane counter gradient of stratified lakes, Magdalena J. Mayr, ISME

A metagenomic assessment of microbial eukaryotic diversity in the global ocean, Aleix Obiol, Mol. Eco. Res.

Ocean acidification affects microbial community and invertebrate settlement on biofilms, Katie S. Nelson, Sci. Rep.

Understanding and creating biocementing beachrocks via biostimulation of indigenous microbial communities, Asha A. Ramachandran , Env. Biotech.

January 16, 2020

Good morning/night everyone!

What I love about writing for MD is the huge diversity of topics we’re meeting along the process of making the daily digest. Even though I’m mostly working on plant and root microbiome, it’s amazing to see how diverse is the world of microbiome and how much more there is to accomplish. Check out today’s digest- and don’t forget the News section as well! it is highly interesting!

General Microbiology

Detection of phylogenetic core groups in diverse microbial ecosystems, Marcos Parras Molto, bioRxiv

Isolation of an archaeon at the prokaryote–eukaryote interface, Hiroyuki Imachi, Nature

Ferrosomes are iron storage organelles formed by broadly conserved gene clusters in bacteria and archaea, Carly R. Grant , bioRxiv

Human microbiome

Distribution of microbial communities and core microbiome in successive wound grades of diabetic foot ulcer individuals, Apoorva Jnana, AEM

Animal microbiome

Parasites modulate the gut-microbiome in insects: A proof-of-concept study, Brian Fredensborg, PlosONE

The effect of diet on the gastrointestinal microbiome of juvenile rehabilitating green turtles (Chelonia mydas), Jennifer Bloodgood ,PlosONE

Rotten-skin disease significantly changed giant spiny frog(Paa spinosa) gut microbiota, Tuoyu He, bioRxiv

Bacterial Biogeography of the Colon in Dogs With Chronic Inflammatory Enteropathy, Paula Giaretta, Veterniary Pathology

Plant and environmental microbiome

Biostimulants applied to maize seeds modulate the enzymatic activity and metaproteome of the rhizosphere, Monica Mattarozzi, Applied Soil Ecology

Biological inhibition of soil nitrification by forest tree species affects Nitrobacter populations, Amandine Laffite, Environmental Microbiology

Extremophile microalgae: An overview, Veronica Malavasi , Journal of Phycology

Methods in microbiome

**Taxonomic classification method for metagenomics based on
core protein families with Core-Kaiju
, Anna Tovo, bioRxiv

**Metagenomic sequencing with spiked primer enrichment for viral diagnostics and genomic surveillance, Xianding Deng , Nature Microbiology

Quantitative PCR provides a simple and accessible method for quantitative microbiota profiling, Ching Jian, PlosONE

The effect of storage conditions on microbial communities in stool, Kristien Nel Van Zyl, PlosONE

Beyond mass spectrometry, the next step in proteomics, Winston and Gregory Timp, Science Advances

Microbiome in the news

Illumina Announces New Sequencing System, Partnership with Roche and Software Suite to Accelerate Adoption of Genomics

Integrating microbiomes into clinical trials – the importance of time

Bayer and Azitra partnership looks to develop skin microbiome products for eczema

**Please read! our mental health is the MOST important thing in our life! Researchers facing ‘shocking’ levels of stress, survey reveals

November 2, 2019

Good Weekend morning for all!

Today’s digest is highly rich with plant and soil microbiome papers (notice a great Science paper regarding soil suppressiveness phenomena), as well as bacterial metabolism papers and more. Have a great and peaceful weekend!

Human and animal microbiome

Studying the gut virome in the metagenomic era: challenges and perspectives, Sanzhima Garmaeva, BMC Biology

Cortisol-induced signatures of stress in the fish microbiome, Tamsyn M Uren Webster, bioRxiv

Influence of pig gut microbiota on Mycoplasma hyopneumoniae susceptibility, Meera Surendran Nair, Veterinary Research

Natural variation in the contribution of microbial density to inducible immune dynamics, Derrick Jent, Molecular Ecology

Metabolism

The ecology and evolution of microbial metabolic strategies, Djordje Bajic & Alvaro Sanchez, Curr. Opin. In. Biotechnology

Is the enzymatic hydrolysis of soil organic phosphorus compounds limited by enzyme or substrate availability?, K.A. Jarosch ,SBB

Plant and Soil microbiome

Pathogen-induced activation of disease-suppressive functions in the endophytic root microbiome, Victor J. Carrio, Science

Drivers of the composition of active rhizosphere bacterial communities in temperate grasslands, Selma Vieira, ISME

Analysis of soil bacterial communities associated with genetically modified drought-tolerant corn, Jose G. Ibaraa ,Applid Soil Ecology

Phyllosphere of Submerged Plants in Bathing Lakes as a Reservoir of Fungi Potential Human Pathogens, Anna Biedunkiewicz, Microbial Ecology

Bacterial microbiome associated with the rhizosphere and root interior of crops in Saskatchewan, Canada, Jorge Cordero, Can. J. of Microbiology

Comparative metagenomics of two distinct biological soil crusts in the Tengger Desert, China, Jin-Yu Li , SBB

In planta bacterial multi-omics analysis illuminates regulatory principles underlying plant-pathogen interactions, Tatsuyas Nobori, bioRxiv

Air microbiome

Microbial communities in the tropical air ecosystem follow a precise diel cycle, Elena S. Gusareva, PNAS

Bioinformatics

Evaluating Bioinformatic Pipeline Performance for Forensic Microbiome Analysis, Kierra F. Kaszubinski, J. o. Forensic Sci.

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

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

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