October 3, 2020

Shalom and good morning from Israel!

Today’s digest is highly diverse, with papers about naming microbes (bottom line- be creative and interesting!), human hair microbiome, the role of one single bacteria in plant growth, how phages weaponizes host bacteria and much more.

Lastly, a bit of ‘self promotion’- the lockdown in Isrel encouraged me to finally create AgrimicroPapers, a twitter-bot (using this great manual) for agriculture- and plant microbiome-realted papers. Feel free to follow and DM papers if they were missed by the bot. Enjoy!

General microbiology

Prokaryotic names: the bold and the beautiful, Aharon Oren, FEMS Micro. Letters

Human and animal microbiome

**Understanding the impact of antibiotic perturbation on the human microbiome, D.J. Schwartz, Genome Medicine

Salivary microbiome in patients undergoing hemodialysis and its associations with the duration of the dialysis, Xiaobo Duan, BMC Nephrology

Phytochemicals as modifiers of gut microbial communities, Giulia Dingedo, Food & Function

Relationship between the bacterial community structures on human hair and scalp, Kota Watanabe, Biosc. Biotech. Bioche

Pangenome sequence evolution within human gut microbiomes is explained by gene-specific rather than host-specific selective pressures, Arnaud N’Guessan, bioRxiv

Changes in dietary fiber intake in mice reveal
associations between colonic mucin Oglycosylation and specific gut bacteria
, Hasinika Gamage, Gut Microbes

Gut metabolites are more predictive of disease- and cohoused- states than gut bacterial features in a mouse model of polycystic ovary syndrome, Bryan Ho, bioRxiv

Environmental microbiome

**A single bacterial genus maintains root growth in a complex microbiome, Omri Finkel, Nature

The Soil-Borne Identity and Microbiome-Assisted Agriculture: Looking Back to the Future, Peter H.A.M Bakker, Molecular Plant (Cell)

Quantification of Extracellular Proteases and Chitinases from Marine Bacteria, Yang Zou, Current Micro.

Characterization of microbial communities in commercial bee pollen used for mass rearing of Bombus impatiens,Vicente D. Moreno Andrade, J. Apicultural Research

Phages

Phages weaponize their bacteria with biosynthetic gene clusters, Anna Dragos, bioRxiv

Microbiome news

Biotechs have big ambitions for the microbiome, SFBT

Core metagenomic functions of the poultry microbiome, Poultry World

September 20, 2020

Shalom from Israel and have a happy Jewish New Year!

As yesterday’s digest was packed with great papers, today’s post is a bit thinner- but still with great material. First, take a look at two virtual and fascinating events to be held in the next months. In addition, you’ll find a mini-review about molecular epidiomiology, locust-related microbiome, a fascinating research paper exploring the actual proportion of sequenced prokaryots and a even a paper focusing on the microbiome of hemp.

Stay healthy, wear a mask.

Events

LMU CAM Strategic Partnership Online Symposium: The role of microbes in plant health: Emerging topics!

ISME Virtual Microbial Ecology Summit

Human microbiome

Gut microbiota, NLR proteins, and intestinal homeostasis, Hao Guo, JEM

*Mini-review- Molecular epidemiology in current times, Burkhard Tummler, Env. Micro.

Animal microbiome

Microbiome-related aspects of locust density-dependent phase transition, Omer Levy, bioRxiv

Environmental microbiome

**Estimate of the sequenced proportion of the global prokaryotic genome, Zheng Zhang, Microbiome

Microbial dark matter filling the niche in hypersaline microbial mats, Hon Lun Wong, Microbiome

Pan‐genome study of Thermococcales reveals extensive genetic diversity and genetic evidence of thermophilic adaption, Chaofang Zhong , Env. Micro.

Plant microbiome

Evaluating the microbiome of hemp, Samuel E. Barnett, Phytobiomes

August 26, 2020

Shalom from Israel! Today’s digest has some great review papers, as well as research articles focusing on citures disease, vaginal microbiome, gut virome and some cool bioinformatic tools.

Also, check out this great event for the soil microbilogists out there: Non-academic Careers in Soil Ecology: a virtual career panel, hosted by MSU.

Enjoy your summer holiday if you managed to get one and as always- find yourself the time to rest and re-energize.

General

**review: Compartmentalization drives the evolution of symbiotic cooperation, Guillaume Chomicki, Phil. Tran. B

Marine microbiomoe

Assessing the strength and sensitivity of the core microbiota approach on a highly diverse sponge reef, Carmen Astudillo-Garica , Env. Micro.

Plant microbiome

Cooperation, Competition, and Specialized Metabolism in a Simplified Root Nodule Microbiome, Bridget L. Hansen , mBio

Stable isotope informed genome-resolved metagenomics uncovers potential trophic interactions in rhizosphere soil, Evan P. Starr, bioRxiv

Disease-Induced Microbial Shifts in Citrus Indicate Microbiome-Derived Responses to Huanglongbing Across the Disease Severity Spectrum, Nichole A. Ginnan , Phytobiomes

Human microbiome and virome

Cervicovaginal Microbiome Composition Is Associated with Metabolic Profiles in Healthy Pregnancy, Andrew Oliver , mBio

The Gut Virome Database Reveals Age-Dependent Patterns of Virome Diversity in the Human Gut, Ann C. Gregory , Cell Host Microbe

Bioinformatics

BiG-SLiCE: A Highly Scalable Tool Maps the Diversity of 1.2 Million Biosynthetic Gene Clusters, Satria Kutsar, bioRxiv

**mini-review: Natural product discovery through microbial genome mining, Emma Kenshole, Cur. Op. Chem. Bio.

Available Benchmarking Bacterial Promoter Prediction Tools: Potentialities and Limitations, Murilo Henrique Anzolini Cassiano, mSystems

June 27, 2020

Shalom from Israel and a Happy world microbiome day!

Yes, it is a true day! celebrating the huge diversity of microbes around us, above us, below us and inside us. Check the day’s official website for more information, and take the weekend to appreciate this amazing field and your own personal contribution to advancing our knowledge about microbial communities on our planet.

Personally, I did my undergrad in Ecology and Evolution, confidence that I’ll my scientific career will focus on plant ecology and distribution, or at least large animals. Microbiology classes and introduction labs bored me, and I did my best to avoid this topic. But all of a sudden, during my Master’s degree (where I worked on a pathogenicity mechanism of postharvest disease-causing bacteria), I fell in love with microbiology in general, and specific bacterial communities. The huge untapped diversity, the unbelievable functions and the amazing interactions needed to maintain a functional community of these invisible inhabitants just fascinated me. Today, as a Ph.D. student exploring secondary metabolites gene clusters in soil and root microbiome, I’m a super-fan of the bacterial world.

How did you end up being microbiome suckers? Feel free to share your stories here as a comment, on MD FB page, or directly on tweeter.

Today’s digest include several microbimoe papers of animal midels (including ‘dirty mice’), diseased tomatoes taxonomical and functional microbiome profile, AND- a sweet reminder of the pre-COVID-19 world, with an analysis of the dust microbiome of a plane (remember this vehicle?).

Human and Animal Models microbiome

**Microbial transmission in animal social networks and the social microbiome, Amar Sarkar , Nat. Eco. Evo.

Does entry to center-based childcare affect gut microbial colonization in young infants?, Gerben D. A. Hermes, Scientific Reports

Serum metabolites reflecting gut microbiome
alpha diversity predict type 2 diabetes
, Cristina Menni, Gut microbes

**New Insights into the Immune System Using Dirty Mice, Sara E. Hamilton, J. Immunology.

Optimization of cerebrospinal fluid microbial metagenomic sequencing diagnostics,Josefin Olausson , bioRxiv

Sleep fragmentation increases blood pressure and is associated with alterations in the gut microbiome and fecal metabolome in rats, Katherine.Maki, Phys. Geno.

Animal microbiome

Environment Shapes the Microbiome of the Blue Orchard Bee, Osmia lignaria, Hamutahl Cohen, Microbial Ecology

The gut mycobiome of healthy mice is shaped by the environment and shapes metabolic outcomes in response to diet, Tahliyah S. Mims, bioRxiv

Microbial communities network analysis of anaerobic reactors fed with bovine and swine slurry, Eliane Cristina Gruszka Vendruscolo, Sci. Tot. Env.

Metagenomic analysis reveals significant differences in microbiome and metabolic profiles in the rumen of sheep fed low N diet with increased urea supplementation, Zhipeng Li, FEMS Micro. Eco.

Soil and Plant microbiome

Changes in Bacterial and Fungal Microbiomes Associated with Tomatoes of Healthy and Infected by Fusarium oxysporum f. sp. lycopersici, Xin Zhou, Microbial Ecology

Insights into drylands biocrust microbiome: geography, soil depth, and crust type affect biocrust microbial communities and networks in Mojave Desert, USA, Nuttapon Pombubpa, FEMS Micro. Eco.

Exploring the Lignin Catabolism Potential of Soil-Derived Lignocellulolytic Microbial Consortia by a Gene-Centric Metagenomic Approach, Laura Díaz-García, Microbial Ecology

Shotgun Metagenomics Of Dust Microbiome From Flight Deck And Cabin In Civil Aviation Aircraft, Yu Sun, Indoor Air

Bioinformatics

MicroNiche: an R package for assessing microbial niche breadth and overlap from amplicon sequencing data, D.R. Finn , FEMS Micro. Eco.

June 09, 2020

Good morning everyone!

Today’s digest presents several antibiotic resistance papers, as well as hospital ICU microbiome study, a microbial nomenculture paper, bunch of human microbiome papers (both gut and vaginal), as well as two computational platforms for analyzing microbial data.

In a more personal note– recently, my PhD research (at ARO and The Hebrew U, Israel) resulted in two manuscripts dealing with the exciting world of bacterial secondary metabolites. The first one is a review paper where we present state-of-the-art tools and methodologies to study and identify novel secondary metabolites gene clusters within the widely diverse soil and root bacterial communities. We present a conceptual pipeline for an efficient use of these culture-based and culture-independent platforms to identify novel antimicrobials-producing gene clusters in-vivo.

The second one (a bioRxiv pre-print) utilized some of these techniques to explore differences in secondary metabolites gene clusters between soil and roots bacterial communities, in terms of diversity, composition and taxonomy. We then took advantage of this data and deeply focused on root-enriched and abundant sequences (those that were associated with NRPS and PKS, mega-enzymes that produces two very important families of secondary metabolites- nonribosomal peptides and polyketides). Then, we used a unique culture-independent platform (eSNaPD, from Sean Brady lab @ Rockefeller U, NY) and were able to actually recover 5 clones (~40Kb in length) that harbored five novel gene clusters. At least one of these probably encode for an antifungal metabolites (derived from Actinobacteria). This piepline/platform is applicable for other uses of course, depending on your research question and the functions you’re intrested in. I’ll be happy for any feedback regarding the bioRxiv MS (either directly there or via my tweeter).

General microbiology

Roadmap for naming uncultivated Archaea and Bacteria, Alison E. Murray, Nature Microbiology

Human microbiome

Re-evaluating the relationship between missing heritability and the microbiome, Gavin Douglas , Microbiome

Microbes and mental health: Can the microbiome help explain clinical heterogeneity in psychiatry?, Christina L. Hayes, Front. Neuroendocrinology

Analysis of 1321 Eubacterium rectale genomes from metagenomes uncovers complex phylogeographic population structure and subspecies functional adaptations, Nicolai Karcher, Genome Biology

Exploring potential of vaginal Lactobacillus isolates from South African women for enhancing treatment for bacterial vaginosis, Anna Ursula Happel , PLOS Pathogens

Hospital microbiome

Temporal variations in bacterial community diversity and composition throughout intensive care unit renovations, Jessica Chopik , Microbiome

Antibiotic Resistance

The household resistome – frequency of beta-lactamases, class 1 integron and antibiotic resistant bacteria in the domestic environment, Laura S. Schages , bioRxiv

Environmental conditions dictate differential evolution of vancomycin resistance in Staphylococcus aureus, Henrique Machado, bioRxiv

Coexistence of Antibiotic Resistance Genes and Virulence Factors Deciphered by Large-Scale Complete Genome Analysis, Yu Pan, mSystems

Bioinformatics

A Framework for Effective Application of Machine Learning to Microbiome-Based Classification Problems, Begum D. Topcuoglu, mBio

PVAmpliconFinder: a workflow for the identification of human papillomaviruses from high-throughput amplicon sequencing, Alexis Robitaille, BMC Bioinformatics

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

December 18, 2019

Good morning/afternoon all microbiome lovers!

Coming back from 4th Thunen Sumposium on Soil Metagenomics (11-13.12, Germany), the first section of today’s digest will highlight some work emphasized during the conference. Pay special attention to Amy Willis work (UoW) dealing with amplification bias in 16S analyses, among else. You are more than welcome to check the conference and the bioinformatic workshops schedule, as you’ll find interesting, inspiring and useful studies and tools that are relevant even if you’re not working on soil-associated habitats.

Have a great day!

Soil Metagenomics insights

Rigorous Statistical Methods for Rigorous Microbiome Science, Amy Willis, mSystems. I highly recommended to be familiar with the Willis lab works and tools, for all of us working with amplicon-sequencing and metagenomics. Amy was kind enough to upload her conference materials to github, using this link.

Additionally, They just started a bio-statistics blog, so check this as well.

Consistent and correctable bias in metagenomic sequencing experiments, Michael R. McLaren, bioRxiv

Understanding and interpreting community sequencing measurements of the vaginal microbiome, HL Berman, BJOG

These two papers are from Benjamin Callahan group (NCSW). Even though he wasn’t at the conference, his work (et al.) were mentioned several times by other speakers, so I decided to emphasize these two papers.

The MG-RAST API explorer: an on-ramp for RESTful query composition, Tobias Paczian, BMC Bioinformatics. Folker Meyer, one of the developers of MG-RAST and its head, was actually at the conference with a great talk about both MG-RAST and the importance of pipelines and common workflow language in computational biology. Check this link and the MG-RAST API explorer, making it so much simpler to search, filter and efficiently use MG-RAST.

TerrestrialMetagenomeDB: a public repository of curated and standardized metadata for terrestrial metagenomes, Felipe B Correa, bioRxiv. An amazing tool for searching and filtering soil-associated metagenomes in different databases, plus simple codes for downloading. Take a look at more papers from the de-Rocha group.

Human microbiomoe

**Molecular messages in human microbiota, Matthew T. Henke and Jon Clardy, Science

Resident microbes of lactation rooms and daycares, Diana H. Taft, PeerJ

Female genital tract microbiota affecting the risk of preterm birth: What do we know so far? A Review, O. Tsonis, European J OBG & Reproductive Biology

Differences in Fecal Microbiomes and Metabolomes of People With vs Without Irritable Bowel Syndrome and Bile Acid Malabsorption, Ian B. Jeffery, Gastroenterology

Soil and Plant microbiome

Comparison of Microbial Community of Rhizosphere and Endosphere in Kiwifruit, Min-Jung Kim, Plant Patho J.

Soil microbial communities in diverse agroecosystems exposed to the herbicide glyphosate, Ryan M. Kepler, AEM

Soil exposed to silver nanoparticles reveals significant changes in community structure and altered microbial transcriptional profiles, Matthew J. Meier, Env. Pollution

Animal microbiome

Effects of disease, antibiotic treatment and recovery trajectory on the microbiome of farmed seabass (Dicentrarchus labrax), Danila Rosado, Scientific Reports