April 2, 2021

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Good morning and happy Friday!

In my last blog post I requested reader contributions and many of you reached out! Below are some of the highlights which include a commentary on phylogenetic core groups, a preprint on viral RNA methylation in Wolbachia, a database for the murine oral bacterial community, and a research article on fungal modification in the leaf-cutter ant fungal garden ecosystem.

Events and jobs

Biological Sciences Laboratory Instructor Position at Smith College in Northampton, MA

General microbiome

***Commentary: Phylogenetic Core Groups: a promising concept in search of a consistent methodological framework – Pascual-García – Microbiome

Animal microbiome

***Preprint: Differential viral RNA methylation contributes to pathogen blocking in Wolbachia-colonized arthropod – Bhattacharya et al. – bioRxiv

Preprint: Isolation and characterization of a novel Wolbachia bacteriophage from Allonemobius socius crickets in Missouri – Fischer et al. – bioRxiv

***From plants to ants: Fungal modification of leaf lipids for nutrition and communication in the leaf-cutter ant fungal garden ecosystem – Khadempour et al. – mSystems

Plant, root, and soil microbiome

Preprint: Experimental evolution-driven identification of Arabidopsis rhizosphere competence genes in Pseudomonas protegens – Zhang et al. – bioRxiv

Built environment

Metagenomic profile of microbial communities in a drinking water storage tank sediment after sequential exposure to monochloramine, free chlorine, and monochloramine – Gomez-Alvarez et al. – ACS EST Water

Bioinformatics

***A 16S rRNA gene and draft genome database for the murine oral bacterial community – Joesph et al. – mSystems

April 1, 2021

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General microbiome

Viral genomic, metagenomic and human transcriptomic characterization and prediction of the clinical forms of COVID-19 – Rodrigez et al. – PLOS Pathogens

A multiomics approach to identify host-microbe alterations associated with infection severity in diabetic foot infections: a pilot study – Radzieta – et al. – NPJ Biofilms and Microbiomes

Pregnancy and early life

Interactions between gut microbiota and metabolites modulate cytokine network imbalances in women with unexplained miscarriage – Liu et al. – NPJ Biofilms and Microbiomes

Developmental trajectory of the healthy human gut microbiota during the first 5 years of life – Roswall et al. – Cell Host & Microbiome

Human gut microbiome

Compositional change of gut microbiome and osteocalcin expressing endothelial progenitor cells in patients with coronary artery disease – Toya et al. – PLOS One

Stool metabolome-microbiota evaluation among children and adolescents with obesity, overweight, and normal-weight using 1H NMR and 16S rRNA gene profiling – Jaimes et al. – PLOS One

Gut dysbiosis and mortality in hemodialysis patients – Lin et al. – NPJ Biofilms and Microbiomes

[REVIEW]The Interplay between Diet, Gut Microbes, and Host Epigenetics in Health and Disease – Shock et al. – The Journal of Nutritional Biochemistry

[REVIEW]Circadian rhythms and the gut microbiome synchronize the host’s metabolic response to diet – Lopez et al. – Cell Metabolism

Animal experiments (mouse/rat experiments, chickens/pigs on different diets)

Meta-analysis identifies the effect of dietary multi-enzyme supplementation on gut health of pigs – Ramani et al. – Scientific Reports

Silicon-containing water intake confers antioxidant effect, gastrointestinal protection, and gut microbiota modulation in the rodents – Wu et al. – PLOS One

Animal microbiome (for animals in the wild)

[PREPRINT]16S rRNA Amplicon Sequencing of Bagworm Metisa plana Walker (Lepidoptera: Psychidae) – Ting et al. – bioRxiv

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

Metagenomic analysis exploring taxonomic and functional diversity of bacterial communities of a Himalayan urban fresh water lake – Ahmad et al. – PLOS One

Geochemical and metagenomics study of a metal-rich, green-turquoise-coloured stream in the southern Swiss Alps – Buetti-Dinh – PLOS One

Phages and viruses

[REVIEW]The human virome: assembly, composition and host interactions – Liang & Bushman – Nature Reviews Microbiology

[PREPRINT]Diverse viruses carrying genes for microbial extremotolerance in the Atacama Desert hyperarid soil – Hwang et al. – bioRxiv

Bioinformatics

MCPdb: The bacterial microcompartment database – Ochoa et al. – PLOS One
[Twitter]97% identity cutoff applied on humans and related species – Matthew Hahn

Techniques

Single strain control of microbial consortia – Fedorec et al. – Nature Communications

Microbes and Art

A Cultural Triumph: Microbiology Student Makes A Petri Dish Masterpiece – McCammon – npr

March 31, 2021

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Pregnancy and early life

Characterization of antimicrobial-resistant Gram-negative bacteria that cause neonatal sepsis in seven low- and middle-income countries – Sands et al. – Nature Microbiology

Human gut microbiome

The Gut Microbiome Is Altered in Postmenopausal Women With Osteoporosis and Osteopenia – Rettedal at al. – JBMR Plus
[Review]Ageing of the gut microbiome: potential influences on immune senescence and inflammageing – Conway & Duggal – Ageing Research Reviews

Human esophageal microbiome

Esophageal microbiome in active eosinophilic esophagitis and changes induced by different therapies – Laserna-Mendieta et al. – Scientific Reports

Animal experiments (mouse/rat experiments, chickens/pigs on different diets)

[PREPRINT]Establishment and Resilience of Transplanted Gut Microbiota in Aged Mice – Wang et al. – bioRxiv

Animal microbiome (for animals in the wild)

Termites Are Associated with External Species-Specific Bacterial Communities – Soukup et al. – Applied and Environmental Microbiology

Plant, root, and soil microbiome

Assessment of fungal diversity in soil rhizosphere associated with Rhazya stricta and some desert plants using metagenomics – Noor et al. – Archives of Microbiology

The temperature sensitivity of soil: microbial biodiversity, growth, and carbon mineralization – Wang et al. – The ISME Journal

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

Recovery of freshwater microbial communities after extreme rain events is mediated by cyclic succession – Shabarova et al. – Nature Microbiology

Techniques

Reduced metagenome sequencing for strain-resolution taxonomic profiles – Snipen et al. – Microbiome

March 30, 2021

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Good morning!

Today’s digest is fairly light, with just a few preprints, so I’d like to do something a bit different today! If you have a recent microbiome-related publication (or have read one that’s particularly exciting) send me a direct message on Twitter (@KaraAnnTinker) or comment on this blog post. If it hasn’t been included on the blog yet, I’ll either update today’s post or cover it on my next blog post later this week.

General microbiome

Preprint: Sulfate adenylyl transferase kinetics and mechanisms of metabolic inhibitors of microbial sulfate respiration – Carlson et al. – bioRxiv

Preprint: Paraburkholderia edwinii protects Aspergillus sp. from phenazines by acting as a toxin sponge – Dahlstrom and Newman – bioRxiv

Plant, root, and soil microbiome

Preprint: Strain diversity of plant-associated Lactiplantibacillus plantarum – Yu et al. – bioRxiv

Water and extremophile microbiome

Preprint: Microbial helpers allow cyanobacteria to thrive in ferruginous waters – Szeinbaum et al. – bioRxiv

March 29th, 2021

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God morgon!

Good morning from Sweden. I know everyone is looking forward to a long weekend, but today is just Monday.

Today’s digest begins with a new visualisation tool for microbiome analysis in R – animalcules. In another study, probiotic yeast metabolites were reported to inhibit bacterial virulence. It is yet another evidence in support of the fermented milk-based probiotic drinks. Talking about the diet, a team of researchers has found the commonly used dietary emulsifiers have a detrimental impact on the gut microbiome. A new study on studying the microbiome using PCR amplification and sequencing illustrates how off-target amplification can introduce a lot of problems. The study in question compared the brain microbiome of healthy individuals and individuals with Parkinson’s disease. Another study has shown how reduced genome provides certain bacteria an advantage in thriving during coastal dinoflagellate blooms.

Elsewhere in the digest are preprints describing a new broad spectrum antifungal, Kenyan traditional medicine as an approach to tackle antibiotic resistance, and prediction of antibiotic resistance using machine learning approach.

Hope you like today’s collection!

Computational Biology

animalcules: interactive microbiome analytics and visualization in R – Yue Zhao, et al., Microbiome

Phylogenetic Core Groups: a promising concept in search of a consistent methodological framework – Alberto Pascual-García, Microbiome

Preprint: Machine-learning prediction of resistance to sub-inhibitory antimicrobial concentrations from Escherichia coli genomes– Sam Benkwitz-Bedford, et al.

Environmental Microbiome

Opportunistic bacteria with reduced genomes are effective competitors for organic nitrogen compounds in coastal dinoflagellate blooms – Yu Han, et al., Microbiome

Metagenomic insights into the taxonomy, function, and dysbiosis of prokaryotic communities in octocorals– T. Keller-Costa, et al., Microbiome

Age and sex-associated variation in the multi-site microbiome of an entire social group of free-ranging rhesus macaques – Mareike C. Janiak, et al., Microbiome

Holo-omics for deciphering plant-microbiome interactions – Ling Xu, et al., Microbiome

General Microbiome

Much ado about nothing? Off-target amplification can lead to false-positive bacterial brain microbiome detection in healthy and Parkinson’s disease individuals – Janis R. Bedarf, et al., Microbiome

Diet and gut microbiome interactions of relevance for symptoms in irritable bowel syndrome – Julien Tap, et al., Microbiome

Cross-kingdom inhibition of bacterial virulence and communication by probiotic yeast metabolites – Orit Malka, et al., Microbiome

Revealing taxon-specific heavy metal-resistance mechanisms in denitrifying phosphorus removal sludge using genome-centric metaproteomics – Yuan Lin, et al., Microbiome

Direct impact of commonly used dietary emulsifiers on human gut microbiota – Sabrine Naimi, et al., Microbiome

Preprint: Paenibacillus sp. strain UY79, isolated from a root nodule of Arachis villosa, displays a broad spectrum of antifungal activity – Andrés Costa, et al.

Bacteria Hysteria

Preprint: Accessory genomic epidemiology of co-circulating Acinetobacter baumannii clones – Valeria Mateo-Estrada, et al.

Preprint: Kenyan Traditional Medicine: Exploring Old Solutions to the Modern Antibacterial Crises Through Natural Products Chemistry – Fidensio K. Ndegwa, et al.

Preprint: The Detection of Bergeyella zoohelcum in Young Children after Cat Bite – Min Hu, et al.

Preprint: Chromatic bacteria version 2 – A Himar1 transposon based delivery vector to extend the host range of a toolbox to fluorescently tag bacteria – Christian F Stocks, et al.

Viruses

Preprint: Human herpesvirus 8 molecular mimicry of ephrin ligands facilitates cell entry and triggers EphA2 signaling – Taylor L. Light, et al.

Preprint: Th17 cell master transcription factor RORC2 regulates HIV-1 gene expression and viral outgrowth – Tomas Raul Wiche Salinas, et al.

Preprint: Rapid evolutionary turnover of mobile genetic elements drives microbial resistance to viruses – Fatima Aysha Hussain, et al.

March 28th, 2021

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Hyvää Päivää from Helsinki, Finland ! Today’s digest contains quite a lot of different topics. If you are interested in marine microbiology and virology, I recommend taking a look at the paper by Gazitúa and collaborators. In this study they investigated the role of phages in shaping the metabolism metabolic networks along redox gradients associated with marine oxygen minimum zones. To do so, they investigated the phage contents in auxiliary metabolic genes involved in bacterial photosynthesis, central carbon metabolism, and nutrient cycling.  

Today’s non-microbiology pick is a web-platform, called Sysrev, built to aid in systematic evidence reviews. Sysrev contains thousands of Findable, Accessible, Iteroperable and Reusable (FAIR) datasets from a large variety of disciplines.

Have a great Sunday!

Human gut microbiome

Preprint: Fecal microbiome of children with norovirus gastroenteritis – Merces Hernandez et al. – bioRxiv 

Plant, root, and soil microbiome

Preprint: Eukaryotic rather than prokaryotic microbiomes change over seasons in rewetted fen peatlands – Wang et al. – bioRxiv 

Plant part and a steep environmental gradient predict plant microbial composition in a tropical watershed. – Bernard et al. – ISME J

Distribution patterns of Acidobacteriota in different fynbos soils – Conradie and Jacobs – PLOS

Water and extremophile microbiome

Preprint: Epidemiological dynamics of viral infection in a marine pico-eukaryote – Listmann et al. – bioRxiv  

Preprint: A deep-sea sulfate reducing bacterium directs the formation of zero-valent sulfur via sulfide oxidation – Liu et al. – bioRxiv

Preprint: Integrated multi-omics investigations reveal the key role of synergistic microbial networks in removing plasticizer di-(2-ethylhexyl) phthalate from estuarine sediments – Ting-Shyang Wei et al. – bioRxiv  

Time-series transcriptomics from cold, oxic subseafloor crustal fluids reveals a motile, mixotrophic microbial community – Seyler et al. – ISME J

Food microbiology

Preprint: Biofilm-forming capacity of Escherichia coli isolated from cattle and beef packing plants: relation to virulence attributes, stage of processing, antimicrobial interventions, and heat tolerance – Stanford et al. – bioRxiv

Phages and viruses

Potential virus-mediated nitrogen cycling in oxygen-depleted oceanic waters – Gazitúa et al. – ISME J

Bioinformatics

Umibato: estimation of time-varying microbial interaction using continuous-time regression hidden Markov model
Shion et al. – bioRxiv

My non-microbiology picks

Preprint: Sysrev: A FAIR Platform For Data Curation And Systematic Evidence Review – Bozada et al. – bioRxiv

March 27, 2021

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Have a nice weekend! Today, in this Digest, we have an interesting review published in Science about microbiome and cancer. We have also articles about different conditions and the effect of the microbiome in the COVID19 vaccine-based immunity. More papers about: microbiome of wild animals,  cow microbiome and glyphosate,  anorexia microbiome in a mice model, and more!

Human and General Microbiome

Review: The microbiome and human cancer – Gregory D. Sepich-Poore – Science

Alterations in mucosa-associated microbiota in the stomach of patients with gastric cancer – Yilin Deng – Cellular Oncology 

Microbial genetic and transcriptional contributions to oxalate degradation by the gut microbiota in health and disease – Menghan Liu – eLife

The gut microbiome in subclinical atherosclerosis: a population-based multi-phenotype analysis – Sibo Zhu – Rheumatology

The microbiome in atopic patients and potential modifications in the context of the severe acute respiratory syndrome coronavirus 2 pandemic – Euna Lee – Current Opinion in Allergy and Clinical Immunology

An observational study of anaerobic bacteria in cystic fibrosis lung using culture dependant and independent approaches – Claudie Lamoureux – Scientific Reports

The Role of Mucosal Immunity and Recombinant Probiotics in SARS-CoV2 Vaccine Development – Shima Moradi-kalbolandi – Probiotics and Antimicrobial Proteins

Propionate catabolism by CD-associated adherent-invasive E. coli counteracts its anti-inflammatory effect – Allison Agus – Gut Microbes

Metabolic Syndrome Cannot Mask the Changes of Fecal Microbiota Compositions Caused by Primary Hepatocellular Carcinoma – Jiajia Ni – Letters in Applied Microbiology

Mendelian Randomization Analysis Reveals Causal Effects of the Human Gut Microbiota on Abdominal Obesity – Qian Xu – The Journal of Nutrition

Animal Microbiome

Diversity and functional landscapes in the microbiota of animals in the wild – Doron Levin – Science

Preliminary functional analysis of the subgingival microbiota of cats with periodontitis and feline chronic gingivostomatitis – Marjory Xavier Rodrigues – Scientific Reports

No hints at glyphosate-induced ruminal dysbiosis in cows – Fabian Billenkamp – npj Biofilms and Microbiomes 

Animal Models

Gut microbial communities from patients with anorexia nervosa do not influence body weight in recipient germ-free mice – Elaine M. Glenny – Gut Microbes

Environmental Microbiome

Invasive freshwater snails form novel microbial relationships – Laura Bankers – Evolutionary Applications

Preprint: Diversity and metagenome analysis of a hydrocarbon-degrading bacterial consortium from asphalt lakes located in Wietze, Germany – Michael O. Eze – Biorxiv

Built Environment

The Impacts of the Occupants on the Bacterial Communities of Classrooms – Zhou Feng – Current Microbiology 

Other

Meta-analysis methods for multiple related markers: Applications to microbiome studies with the results on multiple α-diversity indices – Hyunwook Koh – Statistics in Medicine

March 26, 2021

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Good morning from New Jersey! Tons of papers to share with you today, including three about the role of the microbiome in COVID-19 and multiple new analysis tools and techniques.

Human respiratory microbiome

Functional profiling of COVID-19 respiratory tract microbiomes, Niina Haiminen et al., Scientific Reports

[Preprint] Mild CF Lung Disease is Associated with Bacterial Community Stability, Thomas H. Hampton et al., bioRxiv

Human skin microbiome

[Preprint] On-person adaptive evolution of Staphylococcus aureus during atopic dermatitis increases disease severity, Felix M. Key et al., bioRxiv

Human gut microbiome

[Mini-Review] The Unique Impact of COVID-19 on Human Gut Microbiome Research, Ella Burchill et al., Frontiers in Medicine

Variability in digestive and respiratory tract Ace2 expression is associated with the microbiome, Koester and Li et al., PLOS ONE

[Review] Towards a mechanistic understanding of reciprocal drug–microbiome interactions, Michael Zimmermann et al., Molecular Systems Biology

[Review] The Microbiome Meets Nanotechnology: Opportunities and Challenges in Developing New Diagnostic Devices, Celia Fuentes‐Chust et al., Advanced Materials

[Preprint] The capacity to produce hydrogen sulfide (H2S) via cysteine degradation is ubiquitous in the human gut microbiome, Domenick J Braccia et al., bioRxiv

Model experiments

[Preprint] Species richness determines C. difficile invasion outcome in synthetic human gut communities, Susan Hromada et al., bioRxiv

Gut microbiota determines the social behavior of mice and induces metabolic and inflammatory changes in their adipose tissue, Oryan Agranyoni et al., npj Biofilms and Microbiomes

Improvement of loperamide-induced slow transit constipation by Bifidobacterium bifidum G9-1 is mediated by the correction of butyrate production and neurotransmitter profile due to improvement in dysbiosis, Yutaka Makizaki et al., PLOS ONE

Animal microbiome

A Preliminary Comparison on Faecal Microbiomes of Free-Ranging Large Baleen (Balaenoptera musculus, B. physalus, B. borealis) and Toothed (Physeter macrocephalus) Whales, Stefanie P. Glaeser et al., Microbial Ecology

Host–microbial systems as glass cannons: Explaining microbiome stability in corals exposed to extrinsic perturbations, Courtney M. Dunphy et al., Journal of Animal Ecology

Fish predation on corals promotes the dispersal of coral symbionts, Carsten G. B. Grupstra et al., Animal Microbiome

Plant, root, and soil microbiome

Global analysis of the apple fruit microbiome: Are all apples the same?, Ahmed Abdelfattah et al., Environmental Microbiology

Evaluating domestication and ploidy effects on the assembly of the wheat bacterial microbiome, Wipf and Coleman-Derr, PLOS ONE

Water and extremophile microbiome

[Preprint] Uncharted biosynthetic potential of the ocean microbiome, Lucas Paoli et al., bioRxiv

The microbiome of the Black Sea water column analyzed by shotgun and genome centric metagenomics, Pedro J. Cabello-Yeves et al., Environmental Microbiome

Revealing taxon-specific heavy metal-resistance mechanisms in denitrifying phosphorus removal sludge using genome-centric metaproteomics, Yuan Lin et al., Microbiome

Bioinformatics

Forensic Microbiome Database: A Tool for Forensic Geolocation Meta-Analysis Using Publicly Available 16S rRNA Microbiome Sequencing, Singh and Clarke et al., Frontiers in Microbiology

ProgPerm: Progressive permutation for a dynamic representation of the robustness of microbiome discoveries, Liangliang Zhang et al., BMC Bioinformatics

Model-Based Microbiome Data Ordination: A Variational Approximation Approach, Yanyan Zeng et al., Journal of Computational and Graphical Statistics

Techniques

Blue poo: impact of gut transit time on the gut microbiome using a novel marker, Francesco Asnicar et al., Gut

Benchmarking DNA isolation kits used in analyses of the urinary microbiome, Lisa Karstens et al., Scientific Reports

Choice of library preparation affects sequence quality, genome assembly, and precise in silico prediction of virulence genes in shiga toxin-producing Escherichia coli, Julie Haendiges et al., PLOS ONE

March 24, 2021

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Human gut microbiome

[OPINION]Targeting the Gut Microbiome to Mitigate Immunotherapy-Induced Colitis in Cancer – Chang et al – Trends in Cancer

Direct impact of commonly used dietary emulsifiers on human gut microbiota – Naimi et al. – Microbiome

Animal experiments (mouse/rat experiments, chickens/pigs on different diets)

[REVIEW]Establishing causality in Salmonella-microbiota-host interaction: The use of gnotobiotic mouse models and synthetic microbial communities – Stecher – International Journal of Medical Microbiology

Gut microbiota dysbiosis promotes age-related atrial fibrillation by lipopolysaccharide and glucose-induced activation of NLRP3-inflammasome – Zhang et al. – Cardiovascular Research

Animal microbiome (for animals in the wild)

Composition and structure of the skin microbiota of rorquals off the Eastern South Pacific – Toro et al. – FEMS Microbiology Ecology

Plant, root, and soil microbiome

[PREPRINT]Neural networks and extreme gradient boosting predict multiple thresholds and trajectories of microbial biodiversity responses due to browning – Fontaine et al. – bioRxiv

Comparative microbial antibiotic resistome between urban and deep forest environments – Zheng et al. – Environmental Microbiology Reports

Bioinformatics

[PREPRINT]Genomic characterization of three novel Desulfobacterota classes expand the metabolic and phylogenetic diversity of the Phylum – Murphy et al. – bioRxiv

March 22

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Virome

Hybrid assembly of an agricultural slurry virome reveals a diverse and stable community with the potential to alter the metabolism and virulence of veterinary pathogens – Cook et al. – Microbiome

Plant microbiome

Protists as main indicators and determinants of plant performance – Guo et al. – Microbiome

Rock metagenomes

Pre-Cambrian roots of novel Antarctic cryptoendolithic bacterial lineages – Albanese et al. – Microbiome

Mouse gut microbiome

Xylitol enhances synthesis of propionate in the colon via cross-feeding of gut microbiota – Xiang et al. – Microbiome

Human gut microbiome

Associations between habitual diet, metabolic disease, and the gut microbiota using latent Dirichlet allocation – Breuninger et al. – Microbiome

Maternal gut microbiota reflecting poor diet quality is associated with spontaneous preterm birth in a prospective cohort study – Gershuni et al. – Am J Clin Nutr