July 31, 2020

Today’s digest features studies on hospital-associated bacterial communities on window components, the effect of urbanization on the vaginal microbiota of Amerindians, nitrate as a potential prebiotic for oral health, and the latest news in bioinformatics. Happy reading!

General microbiome

Microbial species interactions determine community diversity in fluctuating environments – Shota Shibasaki – bioRxiv

Review: The host-associated archaeome – Guillaume Borrel – Nature Reviews Microbiology

Oral microbiome

*Nitrate as a potential prebiotic for the oral microbiome – Bob T. Rosier – Scientific Reports

Skin microbiome

Deep skin dysbiosis in vitiligo patients: link with mitochondrial and immune changes – Hanene Bzioueche – medRxiv

Gut microbiome

Review: The microbiome: An emerging key player in aging and longevity– Minhoo Kim and Bérénice A. Benayoun – Translational Medicine of Aging

Immunoglobulin recognition of fecal bacteria in stunted and non-stunted children: findings from the Afribiota study – Kelsey E. Huus – Microbiome

Vaginal microbiome

*Changes in the vaginal microbiota across a gradient of urbanization – Daniela Vargas-Robles – Scientific Reports

Comparison between a novel molecular tool and conventional methods for diagnostic classification of bacterial vaginosis: is integration of the two approaches necessary for a better evaluation? – Margherita Scapaticci – New Microbiologica

Genome-wide mutagenesis identifies factors involved in Enterococcus faecalis vaginal adherence and persistence – Norhan Alhajjar – bioRxiv

Association between Vaginal Bacterial Microbiota and Vaginal Yeast Colonization – McKenna C Eastment – The Journal of Infectious Diseases

Urinary microbiome

Review: The microbiome in urological diseases – Kwang Woo Lee – Investigive and Clinical Urology

Review: FimH and Anti-Adhesive Therapeutics: A Disarming Strategy Against Uropathogens – Meysam Sarshar – Antibiotics

Characterization of urinary microbiome in patients with bladder cancer: Results from a single-institution, feasibility study – Juan Chipollini – Urologic Oncology: Seminars and Original Investigations

Animal microbiome

Resistance to change: AMR gene dynamics on a commercial pig farm with high antimicrobial usage – Jolinda Pollock – Scientific Reports

Vaginal Microbiota Changes During Estrous Cycle in Dairy Heifers – Juan J. Quereda – Frontiers in Veterinary Science

Animal experiment

The gut microbiome switches mutant p53 from tumour-suppressive to oncogenic – Eliran Kadosh – Nature

An Enteric Pathogen Subverts Colonization Resistance by Evading Competition for Amino Acids in the Gut – Gustavo Caballero-Flores – Cell Host & Microbe

Consumption of a Western-Style Diet Modulates the Response of the Murine Gut Microbiome to Ciprofloxacin – Damien J. Cabral – mSystems

Water and extremophile microbiome

Determining the primary sources of fecal pollution using microbial source tracking assays combined with land-use information in the Edwards Aquifer – Jessica Hinojosa – Water Research

Diverse Microorganisms in Sediment and Groundwater Are Implicated in Extracellular Redox Processes Based on Genomic Analysis of Bioanode Communities – Tyler J. Arbour – Frontiers in Microbiology

Food microbiome

Discovering microbiota and volatile compounds of surströmming, the traditional Swedish sour herring – Luca Belleggia – Food Microbiology

Built environment

*Viable bacterial communities on hospital window components in patient rooms – Patrick F. Horve – PeerJ

Microbiome and Metagenome Analyses of a Closed Habitat during Human Occupation – Ganesh Babu Malli Mohan – mSystems

Phages and viruses

Viral Metagenomic Content Reflects Seawater Ecological Quality in the Coastal Zone – Anastasia Tsiola – Viruses

Bioinformatics

Evaluating metagenomics tools for genome binning with real metagenomic datasets and CAMI datasets – Yi Yue – BMC Bioinformatics

Untangling Species-Level Composition of Complex Bacterial Communities through a Novel Metagenomic Approach – Christian Milani – mSystems

Automated prediction and annotation of small proteins in microbial genomes– Matthew G Durrant and Ami S Bhatt – bioRxiv

Accurate and sensitive detection of microbial eukaryotes from metagenomic shotgun sequencing data – Abigail L. Lind – bioRxiv

MicrobeAnnotator: a user-friendly, comprehensive microbial genome annotation pipeline – Carlos A. Ruiz-Perez – bioRxiv

Topological and kernel-based microbial phenotype prediction from MALDI-TOF mass spectra – Caroline Weis – Bioinformatics

NetCoMi: Network Construction and Comparison for Microbiome Data in R – Stefanie Peschel – bioRxiv

Review: Metagenomic approaches in microbial ecology: an update on whole-genome and marker gene sequencing analyses – Ana Elena Pérez-Cobas – Microbial Genomics

Podcast

Machine learning for drug development with Marinka Zitnik – Jacob Schreiber – The Bioinformatics Chat

July 27, 2020

Greetings from Pittsburgh!

Saturday and Sunday’s digests were packed full of great articles, which means the week is off to a slower start than usual. We’ve got two environmentally focused preprints that I am super excited about, a paper demonstrating how microbiota can be dosed in order to help mice mitigate intestinal cancer and inflammation, and a paper focused on the eco-thermodynamics of methanogenic bioprocesses. Enjoy!

Animal experiments

Microbiota from alginate oligosaccharide-dosed mice successfully mitigated small intestinal mucositis – Zhang et al. – Microbiome

Water and extremophile microbiome

Preprint: Distinct microbial communities along the chronic oil pollution continuum of the Persian Gulf converge with oil spill accidents – Somee et al. – BioRxiv

Catabolism and interactions of uncultured organisms shaped by eco-thermodynamics in methanogenic bioprocesses – Nobu et al. – Microbiome

Preprint: Freshwater monitoring by nanopore sequencing – Urban et al. – bioRxiv

July 19, 2020

Hello from the Sonoran Desert! In today’s digest, you’ll find find a lot of very interesting papers! For those interested in host-phages interactions, there is an amazing work from Ping and collaborators looking at phage infections dynamics in migrating bacterial populations. Interestingly, the authors suggests that phages may be able to “hitchhike” with moving bacteria.

To continue with our viral readings, you’ll also find an interesting perspective paper from Kuprovic and collaborators. In this piece, the authors attempt to reconstruct the virome associated to LUCA (Last Universal Cellular Ancestor). Amazingly, their reconstruction shows that a remarkably complex virome would have been associated to LUCA, suggesting an extensive viral evolution antedating LUCA!

Finally, today’s non-microbiology pick is a book, looking at the fascinating Cuatro Ciénegas Basin, located in México, a site that is often described as a real outdoor laboratory for astrobiology. Indeed, the Basin site contains gypsum-rich soil analogous to the Gale Crater in Mars, and the ponds contains extremely oligotrophic waters, which can be used to model ancient oceans chemistry. You’ll explore along the chapters the history, ecology, microbiology and evolution of this amazing site, to unravel the mysteries of this site absolutely unique on the planet.

Have a great Sunday!


Human respiratory microbiome

Review: Insights gained into respiratory infection pathogenesis using lung tissue metabolomics –  Bernatchez and McCall –  PLOS Pathogens

Human gut microbiome

Description and determinants of the faecal resistome and microbiome of farmers and slaughterhouse workers: A metagenome-wide cross-sectional study –  Van Gompel et al. –  Environment International

Review: The influence of the gut microbiome on obesity –  Blanco – Journal of the American Association of Nurse Practitioners


Animal microbiome (for animals in the wild)

Comparative analysis of the gut microbiota of Apis cerana in Yunnan using high-throughput sequencing. –  Luo et al. –  Archives of Microbiology

Plant, root, and soil microbiome

Higher tree diversity increases soil microbial resistance to drought. –  Gillespie et al. –  Communications Biology

Effect of land uses on soil microbial community structures among different soil depths in northeastern China. –  Ji et al. –  European Journal of soil Biology

Structural variability and niche differentiation of the rhizosphere and endosphere fungal microbiome of Casuarina equisetifolia at different ages. –  Huang et al. –  Environmental Microbiology

Water and extremophile microbiome (sea, rivers, lakes, glaciers, permafrost, high-salt)

Substrate regulation leads to differential responses of microbial ammonia-oxidizing communities to ocean warming. –  Zheng et al. –  Nature communications

Diversity and dynamics of relevant nanoplanktonic diatoms in the Western English Channel. –  Arsenieff et al.  –  The ISME Journal

Lake characteristics influence how methanogens in littoral sediments respond to terrestrial litter inputs. –  Yakimovich et al. –  The ISME Journal

Built environment (subways, indoor surfaces)

Heavy metal concentrations in Brazilian port areas and their relationships with microorganisms: can pollution in these areas change the microbial community? –  Del Busso Zampieri et al. –  Environmental Monitoring and Assessment

Food microbiology

Material conversion, microbial community composition and metabolic functional succession during green soybean hull composting. –  Zhang et al. –  Bioresource Technology


Phages and viruses

Hitchhiking, collapse, and contingency in phage infections of migrating bacterial populations. –  Ping et al. – The ISME Journal

Review: The LUCA and its complex virome. –  Krupovic et al. –  Nature Review Microbiology

Insights into the dynamics between viruses and their hosts in a hot spring microbial mat. –  Jarett et al. –  ISME Journal

Bioinformatics

IDMIL: an alignment-free Interpretable Deep Multiple Instance Learning (MIL) for predicting disease from whole-metagenomic data. –  Rahman and Rangwala –  Bioinformatics


My non-microbiology pick

Book: Astrobiology and Cuatro Ciénegas Basin as an Analog of Early Earth. –  Medina-Chávez et al. –  Cuatro Ciénegas Basin: An Endangered Hyperdiverse Oasis. Springer

July 15, 2020

There are several notable entries in today’s digest. Registration is open for the European Learning Laboratory for the Life Sciences’ “Introducing Your Microbiome” virtual training course. The course is for European secondary school science teachers and is 5 weeks long. The 3rd Microbiome Movement will also be held this year, both virtually and in-person. Links are in the Events section.  

Today I’ve highlighted a bioinformatics paper on variant calling for cpn60 barcode sequencing and an early life paper on pre-term infant stem cell proliferation upregulated by microbial metabolites. While putting this digest together, I learned algae turns snow different colors! This is so cool to me that I’ve highlighted that paper as well. Finally, the News section includes an article for Smithsonian Magazine by Rob Dunn on quarantine’s effects on our microbial passengers.  

Happy reading!

Events

3rd Microbiome Movement – Animal Health & Nutrition Summit, taking place in North Carolina as well as digitally October 19-21, 2020.

European Learning Laboratory for the Life Sciences’ “Introducing Your Microbiome” November 2-December 7, 2020. Applications are due October 15 and the course is free.

Pregnancy and early life

Gut microbiota maturation during early human life induces enterocyte proliferation via microbial metabolites – Michael W. Dougherty – BMC Microbiology

Human gut microbiome

Perspective: Gut microbiome, big data and machine learning to promote precision medicine for cancer – Giovanni Cammarota – Nature Reviews Gastroenterology & Hepatology

Microbiome of death

Characterizing the postmortem human bone microbiome from surface-decomposed remains – Alexandra L. Emmons – PloS One

Animal experiments

Saccharomyces cerevisiae fermentation products (SCFP) stabilize the ruminal microbiota of lactating dairy cows during periods of a depressed rumen pH – Hein M. Tun – BMC Veterinary Research

Animal microbiome

A Shift Pattern of Bacterial Communities Across the Life Stages of the Citrus Red Mite, Panonychus citri – Zhen-yu Zhang – Frontiers in Microbiology

Plant, root, and soil microbiome

Nitrogen enrichment stimulates wetland plant responses whereas salt amendments alter sediment microbial communities and biogeochemical responses – Mary Donato – PloS One

Bioavailable metal (loid) s and physicochemical features co-mediating microbial communities at combined metal (loid) pollution sites – Jiawen Wang – Chemosphere

Assessing the effects of tylosin fermentation dregs as soil amendment on macrolide antibiotic resistance genes and microbial communities: Incubation study – Bo Zhang – Journal of Environmental Science and Health, Part B

Book: Phytobiomes: Current Insights and Future Vistas – Manoj Kumar Solanki – Springer

Early changes in bacterial communities in wound tissues of Pinus massoniana after inoculation with Bursaphelenchus xylophilus – Jinyan Liu – Nematology

Preprint: Unexpected diversity of CPR bacteria and nanoarchaea in the rare biosphere of rhizosphere-associated grassland soil – Alexa M. Nicolas – bioRxiv

Preprint: A Meta-analysis of the known Global Distribution and Host Range of the Ralstonia Species Complex – Tiffany Lowe-Power – bioRxiv

Water, air, and extremophile microbiome

Lipid Biomarker Record of the Serpentinite-Hosted Ecosystem of the Samail Ophiolite, Oman and Implications for the Search for Biosignatures on Mars – Sharon A Newman – Astrobiology

Metabolic acclimation of anammox consortia to decreased temperature – Tangran Huo – Environment International

Complete Genome Sequences of Two Marine Biofilm Isolates, Leisingera sp. nov. Strains 201A and 204H, Novel Representatives of the Roseobacter Group – Giselle S. Cavalcanti – Microbiology Resource Announcements

Microbial interspecific interaction and nitrogen metabolism pathway for the treatment of municipal wastewater by iron carbon based constructed wetland – Xiao Huang – Bioresource Technology

Biogeographical distribution of dissimilatory nitrate reduction to ammonium (DNRA) bacteria in wetland ecosystems around the world – Huawei Pan – Journal of Soils and Sediments

Molecular diversity of the microbial community in coloured snow from the Fildes Peninsula (King George Island, Maritime Antarctica) – Wei Luo – Polar Biology

Novel arsenic hyper-resistant bacteria from an extreme environment, Crven Dol mine, Allchar, North Macedonia – Vladimir Bermanec – Journal of Hazardous Materials

Built environment

Ozone treatment in a wind tunnel for the reduction of airborne viruses in swine buildings – Jonathan M. Vyskocil – Aerosol Science and Technology

Food microbiology

Correlation between microbial communities and key flavors during post-fermentation of Pixian broad bean paste – Ping Liu – Food Research International

Additives affect the distribution of metabolic profile, microbial communities and antibiotic resistance genes in high-moisture sweet corn kernel silage – Zhe Wu – Bioresource Technology

Shifts in autochthonous microbial diversity and volatile metabolites during the fermentation of chili pepper (Capsicum frutescens L.) – Xinxing Xu – Food Chemistry

Proteomic characterization of extracellular vesicles produced by several wine yeast species – Ana Mencher – Microbioal Biotechnology

Book Chapter: Role of Microbes for Attaining Enhanced Food Crop Production – Pankaj Sharma – Microbial Biotechnology: Basic Research and Applications

Bioinformatics

Evaluation of variant calling for cpn60 barcode sequence-based microbiome profiling – Sarah J. Vancuren – PloS One

Techniques

Preprint: Visualization of giant virus particles using BONCAT labeling and STED microscopy – Monica Berjon-Otero – bioRxiv

Microbes in the News

Human Microbiome: 39 trillion microbes and bacteria that call us home – Mun-Keat Looi – Science Focus

What Quarantine is Doing to Your Body’s Wondrous World of Bacteria – Rob Dunn – Smithsonian Magazine

July 3rd, 2020

General microbiome

Microbiome definition re-visited: old concepts and new challenges – Berg et al. Microbiome

Large-scale metabolic interaction network of the mouse and human gut microbiota. – Lim et al. Scientific Data

Early life microbiome

Very early-life exposure to microbiota-induced TNF drives the maturation of neonatal pre-cDC1 – Kohler et al. Gut.

Human gut microbiome

Arrhythmic Gut Microbiome Signatures Predict Risk of Type 2 Diabetes – Reitmeier et al. Cell Host & Microbe

Ranking microbiome variance in inflammatory bowel disease: a large longitudinal intercontinental study – Clooney et al. Gut

Cholesterol Metabolism by Uncultured Human Gut Bacteria Influences Host Cholesterol Level – Kenny et al. Cell Host & Microbe

Amending microbiota by targeting intestinal inflammation with TNF blockade attenuates development of colorectal cancer – Yang et al. Nature Cancer

Animal microbiome

A Systematic Analysis of Mosquito-Microbiome Biosynthetic Gene Clusters Reveals Antimalarial Siderophores that Reduce Mosquito Reproduction Capacity – Ganley et al. Cell Chemical Biology

Extremophile microbiome

Microbial succession during the transition from active to inactive stages of deep-sea hydrothermal vent sulfide chimneys – Hou et al. BMC Microbiome

Phages and viruses

Phase-variable capsular polysaccharides and lipoproteins modify bacteriophage susceptibility in Bacteroides thetaiotaomicron – Porter et al. Nature Microbiology

Bioinformatics

ATLAS: a Snakemake workflow for assembly, annotation, and genomic binning of metagenome sequence data – Kieser et al. BMC Bioinformatics

Techniques

High-Throughput Stool Metaproteomics: Method and Application to Human Specimens – Gonzalez et al. mSystems

Interindividual Variation in Dietary Carbohydrate Metabolism by Gut Bacteria Revealed with Droplet Microfluidic Culture – Villa et al. mSystems

June 16, 2020

Sorry for the late afternoon digest. We are in the midst of trying to get our lab back up and running! There are several interesting papers today, including a commentary on the holobiont model and the usefulness of integrating microbiome and GWAS data, the development of a “Microbiome-Derived Metabolism Screen” for personalized medicine published in Cell, and a paper investigating phylosymbiosis in the skin microbiome of fish. My non-microbiology pick is a urine sampling method to assess diet, which could be very useful to gut microbiome scientists.

General microbiome

Commentary: Re-evaluating the relationship between missing heritability and the microbiome – Gavin M. Douglas – Microbiome

Book chapter: Pharmacomicrobiomics – Weihua Huang – Pharmacogenomics in Precision Medicine

Human gut microbiome

Review: Altered Composition of Gut Microbiota in Depression: A Systematic Review – Zahra Amirkhanzadeh Barandouzi – Frontiers in Psychiatry

Review: Tryptophan Metabolites Along the Microbiota-Gut-Brain Axis: An Interkingdom Communication System Influencing the Gut in Health and Disease – Annalisa Bosi – International Journal of Tryptophan Research

Personalized Mapping of Drug Metabolism by the Human Gut Microbiome – Bahar Javdan – Cell

Bacteroides thetaiotaomicron-derived outer membrane vesicles promote regulatory dendritic cell responses in health but not in inflammatory bowel disease – Lydia Durant – Microbiome

Animal microbiome

The skin microbiome of elasmobranchs follows phylosymbiosis, but in teleost fishes, the microbiomes converge – Michael P. Doane – Microbiome

Whole-genome sequence analysis of environmental Escherichia coli from the faeces of straw-necked ibis (Threskiornis spinicollis) nesting on inland wetlands – Ethan R Wyrsch – Microbial Genomics

Intestinal Microbiota Analyses of Litopenaeus vannamei During a Case of Atypical Massive Mortality in Northwestern Mexico – Alejandro López-Cortés – Current Microbiology

Identification of hepatitis C virus in the common bed bug–a potential, but uncommon route for HCV infection? – Jiaxin Ling – Emerging Microbes & Infections

Eggshell and environmental bacteria contribute to the intestinal microbiota of growing chickens – Joel J. Maki – Journal of Animal Science and Biotechnology

Topography of the respiratory tract bacterial microbiota in cattle – Christopher McMullen – Microbiome

Plant, root, and soil microbiome

Exploring slope spatial heterogeneity by nitrogen transfer and arbuscular mycorrhizal community – Yanyan Yu – Journal of Soils and Sediments

Disentangling drivers of soil microbial potential enzyme activity across rain regimes: An approach based on the functional trait framework – Gabin Piton – Soil Biology and Biochemistry

Microbial communities in petroleum-contaminated seasonally frozen soil and their response to temperature changes – Xusheng Wang – Chemosphere

Review: The Plant Microbiome: From Ecology to Reductionism and Beyond – Connor R. Fitzpatrick – Annual Review of Microbiology

Biogeographic patterns of microbial co-occurrence ecological networks in six American forests – Qichao Tu – Soil Biology and Biochemistry

Water, air, and extremophile microbiome

Microbial communities of container aquatic habitats shift in response to Culex restuans larvae – Ephantus J. Muturi – FEMS Microbiology Ecology

Climate mediates continental scale patterns of stream microbial functional diversity – Félix Picazo – Microbiome

Bacterial diversity of a high-altitude permafrost thaw pond located on Ojos del Salado (Dry Andes, Altiplano-Atacama region) – Júlia Margit Aszalós – Astrobiology  

Effects of active volcanism on bacterial communities in the highest-altitude crater lake of Ojos del Salado (Dry Andes, Altiplano-Atacama Region) – Júlia Margit Aszalós – Astrobiology  

Methanogenesis in the Lake Elton saline aquatic system – Anna Kallistova – Extremophiles

Auxotrophic interactions: A stabilizing attribute of aquatic microbial communities? – Winifred Johnson – FEMS Microbiology Ecology

Food microbiology

Lactic acid accumulation under heat stress related to accelerated glycolysis and mitochondrial dysfunction inhibits the mycelial growth of Pleurotus ostreatus – Zhiyu Yan – Applied Microbiology and Biotechnology

Evaluation and comparison of the microbial communities and volatile profiles in homemade suansun from Guangdong and Yunnan provinces in China – Qianqian Guan – Journal of the Science of Food and Agriculture


Non-Microbiology Pick

Developing community-based urine sampling methods to deploy biomarker technology for the assessment of dietary exposure – Amanda J. Lloyd – Public Health Nutrition

June 08, 2020

Today, we present a broad spectrum of new studies covering among others the mycobiome of human milk, gut microbes and their association with brain development and cognitive function, and a catalogue of previously unseen microbial genomes. Of particular interest is a study that integrates different sources of data to model a personalized gut microbiome. Last but not least we selected a pre-print on the design and characterization of multiepitopes vaccine for SARS-CoV.

General microbiome

Cultivation-independent and cultivation-dependent metagenomes reveal genetic and enzymatic potential of microbial community involved in the degradation of a complex microbial polymer – Costa et al. – Microbiome

REVIEW: Conceptualizing the vertebrate sterolbiome – Ridlon – Applied and Environmental Microbiology

Human milk mycobiome

Human milk fungi: environmental determinants and inter-kingdom associations with milk bacteria in the CHILD Cohort Study – Moossavi et al. – BMC Microbiology

Human skin microbiome

Skin microbiota analysis-inspired development of novel anti-infectives – Liu et al. – Microbiome

Human vaginal microbiome

PREPRINT: Vaginal microbiota of adolescents and their mothers: A preliminary study of vertical transmission and persistence – Bassis – bioRxiv

Human gut microbiome

Personalized whole‐body models integrate metabolism, physiology, and the gut microbiome – Thiele et al. – Mol Syst Biol

REVIEW: The gut microbiota profile of adults with kidney disease and kidney stones: a systematic review of the literature – Stanford et al. – BMC Nephrology

PREPRINT: Gut microbes and their genes are associated with brain development and cognitive function in healthy children – Bonham et al. – bioRxiv

Animal microbiome (for animals in the wild)

Microbial environment shapes immune function and cloacal microbiota dynamics in zebra finches Taeniopygia guttata – van Veelen et al. – Animal Microbiome

PREPRINT: Large scale metagenome assembly reveals novel animal-associated microbial genomes, biosynthetic gene clusters, and other genetic diversity – Youngblut – bioRxiv

Water and extremophile microbiome (sea, rivers, lakes, glaciers, permafrost, high-salt)

Novel insights into the Thaumarchaeota in the deepest oceans: their metabolism and potential adaptation mechanisms – Zhong et al. – Microbiome

The role of metal contamination in shaping microbial communities in heavily polluted marine sediments – Di Cesare et al. – Environmental Pollution

Techniques

Engineering CRISPR/Cas9 to mitigate abundant host contamination for 16S rRNA gene-based amplicon sequencing – Song & Xie – Microbiome

SARS-CoV-2

PREPRINT: In silico design and characterization of multiepitopes vaccine for SARS-CoV from its Spike proteins – Kathwate – bioRxiv

June 2, 2020

Happy Month of June to all,
June serves as the national month for Alzheimer’s and brain awareness. So I will start today’s digest with some news articles about the same.
Further the digest covers some very fascinating research articles about how the microbiome influences transcriptional profile in Drosophila melanogaster to peripheral blood microbial signatures in COPD. Digest also features some awesome microbe related science communication articles.
Enjoy reading!!!
Have a Safe, Healthy, Happy, and Productive month ahead.


Alzheimer’s and brain awareness news posts

Alzheimer’s & Brain Awareness Month 2020 – Bankston – ASBMB Today

Could the gut microbiome be linked to autism? – Svoboda – Nature Outlook

General microbiome
*Interactions between the microbiome and mating influence the female’s transcriptional profile in Drosophila melanogaster – Delbare et al – bioRxiv

Phenotypic changes of bacteria through opportunity and global methylation leads to antibiotic resistance – Neerathilingam et al – bioRxiv

Human nearly-sterile sites
Peripheral blood microbial signatures in COPD – Morrow et al – bioRxiv

Human gut microbiome
Prebiotics and community composition influence gas production of the human gut microbiota – Yu et al – bioRxiv

Short-term High Intensity Interval Training (HIIT) Exercise Does Not Affect Gut Bacterial Community Diversity or Composition of Lean and Overweight Men -Rettedal et al – Experimental Physiology

Animal experiments
Integrative omics analysis of the termite gut system adaptation to Miscanthus diet identifies lignocellulose degradation enzymes – Clusinska et al – Communications Biology

Water and extremophile microbiome
Phylum-level Diversity of the Microbiome of the Extremophilic Basidiomycete Fungus Pisolithus Arhizus (Scop.) Rauschert: An Island of Biodiversity in a Thermal Soil Desert – Culling et al – MicrobiologyOpen

Food microbiology
Lactobacillus Rhamnosus 2016SWU.05.0601 Regulates Immune Balance in Ovalbumin-Sensitized Mice by Modulating the Immune-Related Transcription Factors Expression and Gut Microbiota – Song et al – Journal of the Science of Food and Agriculture

Techniques
Harnessing Ultrasound-Stimulated Phase Change Contrast Agents to Improve Antibiotic Efficacy Against Methicillin-Resistant Staphylococcus aureus Biofilms – Durham et al – bioRxiv

Microbiome Science communication articles
The hunt for a healthy microbiome – Eisenstein – Nature Outlook

The complex relationship between drugs and the microbiome – Savage -Nature Outlook

The Infant Gut Microbiome and Probiotics that Work – Smilowitz and Taft – The Scientist

May 22, 2020

We’ve got a decently sized digest today with a lot of environmental microbe papers, including descriptions of novel species. There is also the Cell paper (highlighted) from Peter Turnbaugh’s group on ketogenic diets and the gut microbiome, which has been getting a lot of press. For new bioinformatic and other techniques, we have a new R package to predict functional profiles in Tax4Fun2, an assessment of phylogenetic rooting methods for bacteria, and a description of fiber intervention used in undergraduate classes for active learning.

 Have a great weekend!

Events

Today is the last day of the Virtual Microbiome Summit.

Pregnancy and early life

Women’s multisite microbial modulation during pregnancy – Luiz G. Sparvoli – Microbial Pathogenesis

Multi-site human microbiome

Review: Bi-Directional Interactions Between Microbiota and Ionizing Radiation in Head and Neck and Pelvic Radiotherapy-Clinical Relevance – Nidhya Teresa Joseph – International Journal of Radiation Biology

Human oral microbiome

Defining the oral microbiome by whole-genome sequencing and resistome analysis: the complexity of the healthy picture – Elisabetta Caselli – BMC Microbiology

Human gut microbiome

Ketogenic diets alter the gut microbiome resulting in decreased intestinal Th17 cells – Qi Yan Ang – Cell

Preprint: Host genetic and environmental factors shape the human gut resistome – Caroline I. Le Roy – bioRxiv

MinION Sequencing of colorectal cancer tumour microbiomes—A comparison with amplicon-based and RNA-Sequencing – William S. Taylor – PLOS One (Originally posted to the Digest as a pre-print, now published)

Animal experiments

Broilers divergently selected for digestibility differ for their digestive microbial ecosystems – Marion Borey – PLOS One

Dietary Isomalto/Malto‐Polysaccharides Increase Fecal Bulk and Microbial Fermentation in Mice – Rima H. Mistry – Molecular Nutrition and Food Research

Longitudinal Effects of Dietary Oxidized Lipids on the Gut Microbiome and Mycobiome in Pigs – Folagbayi Arowolo – FASEB Journal

Animal microbiome

Single-cell amplicon sequencing reveals community structures and transmission trends of protist-associated bacteria in a termite host – Michael E. Stephens – PLOS One

Plant, root, and soil microbiome

Xylella fastidiosa subsp. pauca and olive produced lipids moderate the switch adhesive versus non-adhesive state and viceversa – Valeria Scala – PLOS One

Mitochondrial genome sequence of Phytophthora sansomeana and comparative analysis of Phytophthora mitochondrial genomes – Guohong Cai – PLOS One

nirS-type denitrifying bacterial communities in relation to soil physicochemical conditions and soil depths of two montane riparian meadows in North China. – Xiaoli Han – Environmental Science and Pollution Research

Tissue-Specific Dynamics in the Endophytic Bacterial Communities in Arctic Pioneer Plant Oxyria digyna – Cindy Given – Frontiers in Plant Science

Effects of Cultured Root and Soil Microbial Communities on the Disease of Nicotiana tabacum Caused by Phytophthora nicotianae – Tianbo Liu – Frontiers in Microbiology

Novel putative rhizobial species with different symbiovars nodulate Lotus creticus and their differential preference to distinctive soil properties – M Rejili – FEMS Microbiology Letters

Water, air, and extremophile microbiome

The microbiome of alpine snow algae shows a specific inter-kingdom connectivity and algae-bacteria interactions with supportive capacities – Lisa Krug – ISME Journal

Variation of near surface atmosphere microbial communities at an urban and a suburban site in Philadelphia, PA, USA – JD Stewart – Science of the Total Environment

Pilot-scale petroleum refinery wastewaters treatment systems: performance and microbial communities’ analysis – Fatma Karray – Process Safety and Environmental Protection

Adverse effects of levofloxacin and oxytetracycline on aquatic microbial communities – Zhigao Zhou – Science of the Total Environment

Application of microbial network analysis to discriminate environmental heterogeneity in Fildes Peninsula, Antarctica – Qian Liu – Marine Pollution Bulletin

Tools for successful proliferation: diverse strategies of nutrient acquisition by a benthic cyanobacterium – HS Tee – ISME Journal

Metabolic diversity and co-occurrence of multiple Ferrovum species at an acid mine drainage site – Christen L. Grettenberger – BMC Microbiology

Halocatena pleomorpha gen. nov. sp. nov., an extremely halophilic archaeon of family Halobacteriaceae isolated from saltpan soil – Ashish Verma – IJSEM

Unveiling Cultivable and Uncultivable Halophilic Bacteria Inhabiting Marakkanam Saltpan, India and Their Potential for Biotechnological Applications – Jojy John – Geomicrobiology Journal

Flavobacterium profundi sp. nov., isolated from a deep-sea seamount – Qian Wang – IJSEM

Food microbiology

Molecular epidemiology, genetic diversity and antimicrobial resistance of Staphylococcus aureus isolated from chicken and pig carcasses, and carcass handlers – Onyinye J. Okorie-Kanu – PLOS One

Traditional milk transformation schemes in Côte d’Ivoire and their impact on the prevalence of Streptococcus bovis complex bacteria in dairy products – Aimé R Sanhoun – PLOS One

Comparison of Microbial Communities and Amino Acid Metabolites in Different Traditional Fermentation Starters Used during the Fermentation of Hong Qu Glutinous Rice Wine – Zhang-Cheng Liang – Food Research International

Preprint: Monitoring the microbiome for food safety and quality using deep shotgun sequencing – Kristen L. Beck – bioRxiv

Viruses

Are pangolins the intermediate host of the 2019 novel coronavirus (SARS-CoV-2)? – Ping Liu – PLOS Pathogens

Vector competence of Aedes aegypti from New Caledonia for the four recent circulating dengue virus serotypes – Olivia O’Connor – PLOS Neglected Tropical Diseases

Bioinformatics

Tax4Fun2: prediction of habitat-specific functional profiles and functional redundancy based on 16S rRNA gene sequences – Franziska Wemheuer – Environmental Microbiome

Techniques

Assessing the accuracy of phylogenetic rooting methods on prokaryotic gene families – Taylor Wade – PLOS One

Science education techniques: Fiber Force: A Fiber Diet Intervention in an Advanced Course-Based Undergraduate Research Experience (CURE) Course – Julia Massimelli Sewall – Journal of Microbiology & Biology Education

Science and art

This photographer creates prints with algae.

Non-microbiology picks:

Herd of fuzzy green “glacier mice” baffles scientists.

May 20, 2020

Greetings from Pittsburgh, PA!

Television and movies are a welcome distraction from the current global pandemic. For this digest, I’d like to highlight two articles. The article by Sajjad et al. investigates the possibility of resurrection of ancient microbes present in the natural frozen world and is a perfect pair for the monster-of-the-week X-Files episode “Ice.” The second highlighted article focuses on the microbiome present on two ancient Slavonic parchment codices and how this data can be used to provide additional historical context. Maybe Harrison Ford can team up with Piñar et al. to create a fourth movie in the Indiana Jones Franchise based on their work?

Happy reading, everyone!

General microbiome

Effect of a novel synbiotic on Streptococcus mutans – Bijle et al. – Nature Scientific Reports

Culturomics‐based genomics sheds light on the ecology of the new haloarchaeal genus Halosegnis – Durán‐Viseras et al. – Environmental Microbiology

Review: Ecological features of the persistence of Vibrio cholerae: retrospective analysis and actual state of the problem – Menshikova et al. – Jounral of microbiology, epidemiology, and immunobiology

Metagenome-assembled genomes reveal unique metabolic adaptations of a basal marine Thaumarchaeota lineage – Reji and Francis – ISME Journal

Homoplastic single nucleotide polymorphisms contributed to phenotypic diversity in Mycobacterium tuberculosis – Tantivitayakul et al. – Nature Scientific Reports

Plant, root, and soil microbiome

Impacts of forest conversion to plantations on the soil carbon and nitrogen dynamics, and microbial communities – Wang et al. – Soil Biology and Biochemistry

Water and extremophile microbiome

Novel yeast taxa from the cold: description of Cryolevonia giraudoae sp. nov. and Camptobasidium gelus sp. nov. – de Garcia et al. – International Journal of Systematic and Evolutionary Microbiology

Remote sensing reveals Antarctic green snow algae as important terrestrial carbon sink – Gray et al. – Nature Communications

Review: Resurrection of inactive microbes and resistome present in the natural frozen world: Reality or myth? – Sajjad et al. – Science of the Total Environment

Built environment

Decoding the biological information contained in two ancient Slavonic parchment codices: an added historical value – Piñar et al. – Environmental Microbiology

Bioinformatics

Preprint: Efficiently processing amplicon sequencing data for microbial ecology with dadasnake, a DADA2 implementation in Snakemake – Weißbecker et al. – bioRxiv

Techniques

Editorial: Visualizing the invisible: class excursions to ignite children’s enthusiasm for microbes – McGenity et al. – Microbial Biotechnology

Discovery of thermophilic Bacillales using reduced-representation genotyping for identification – Talamantes-Becerra et al. – BMC Microbiology