Category Archives: Water microbiome

November 12, 2021

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Today’s digest features the study on the Amazon River microbiome, Spanish gut microbiome, review on nanopore sequencing, 16S rRNA metabarcoding study to characterize the responses of the active gut microbiome of fathead minnows to exposure with a model contaminant (benzo[a]pyrene), and more. Happy Friday!

Lung microbiome

Review: The composition of lung microbiome in lung cancer: a systematic review and meta-analysis – Sadaf Najafi – BMC Microbiology

Skin microbiome

Charting host-microbe co-metabolism in skin aging and application to metagenomics data – Wynand Alkema – PlosOne

Gut microbiome

*The Spanish gut microbiome reveals links between microorganisms and Mediterranean diet – Adriel Latorre-Pérez – Scientific Reports

Autism-related dietary preferences mediate autism-gut microbiome associations – Chloe X. Yap – Cell

Animal microbiome

*16S rRNA metabarcoding unearths responses of rare gut microbiome of fathead minnows exposed to benzo[a]pyrene – Abigail DeBofsky – Science of The Total Environment

Sampling the fish gill microbiome: a comparison of tissue biopsies and swabs – Morag Clinton – BMC Microbiology

Rabbit microbiota across the whole body revealed by 16S rRNA gene amplicon sequencing – Xiaofen Hu – BMC Microbiology

Animal experiment

The composition of human vaginal microbiota transferred at birth affects offspring health in a mouse model – Eldin Jašarević – Nature Communications

Polyamine metabolism links gut microbiota and testicular dysfunction – Qi Zhao – Microbiome

A fiber-deprived diet causes cognitive impairment and hippocampal microglia-mediated synaptic loss through the gut microbiota and metabolites – Hongli Shi – Microbiome

Water microbiome

*Microbial population genomes from the Amazon River reveal possible modulation of the organic matter degradation process in tropical freshwaters – Célio Dias Santos-Júnior – Molecular Ecology

Bioinformatics

*Review: Nanopore sequencing technology, bioinformatics and applications – Yunhao Wang – Nature Biotechnology

mBodyMap: a curated database for microbes across human body and their associations with health and diseases – Hanbo Jin – Nucleic Acids Research

Density-based binning of gene clusters to infer function or evolutionary history using GeneGrouper – Alexander G McFarland – Bioinformatics

OptiFit: an improved method for fitting amplicon sequences to existing OTUs – Kelly L Sovacool – bioRxiv

November 10, 2021

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Human urinary tract microbiome

[PREPRINT]Recurrent urinary tract infection and estrogen shape the taxonomic ecology and functional potential of the postmenopausal urobiome – Neugent et al. – bioRxiv

Human gut microbiome

The Impact of a Mediterranean Diet on the Gut Microbiome in Healthy Human Subjects: A Pilot Study – Rejeski et al. – Digestion

Altered diversity and composition of gut microbiota in patients with allergic rhinitis – Zhou et al. – Microbial Pathogenesis

Fecal Microbiome Transplantation for Recurrent Clostridioides difficile Infection: Treatment Efficacy, Short and Long-term Follow-up Results from Consecutive Case Series – Urbonas et al. – Journal of Gastrointestinal and Liver Diseases

Donor screening for fecal microbiota transplantation in China: Evaluation of 8,483 candidates – Zhang et al. – Gastroenterology

Faecal microbial biomarkers in early diagnosis of colorectal cancer – Olovo et al. – Journal of Cellular and Molecular Medicine

Hepatocellular Cancer and Gut Microbiome: Time to Untie Gordian’s Knot – Aygün & Tözün – Journal of Gastrointestinal Cancer

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

Cinnamic acid suppresses bone loss via induction of osteoblast differentiation with alteration of gut microbiota – Hong et al. – The Journal of Nutritional Biochemistry

Gut microbiome affects the metabolism of metronidazole in mice through regulation of hepatic cytochromes P450 expression – Zemanová et al. – PLOS One

Animal microbiome (for animals in the wild)

[PREPRINT]Maternal effects on early-life gut microbiome maturation in a wild nonhuman primate – Baniel et al. – bioRxiv

Evidence of MHC class I and II influencing viral and helminth infection via the microbiome in a non-human primate – Montero et al. – PLOS Pathogens

Gut Microbiome of Wild Baltic Salmon (Salmo salar L.) Parr – Skrodenytė-Arbačiauskienė – Microbial Ecology

Plant, root, and soil microbiome

Artificial selection of stable rhizosphere microbiota leads to heritable plant phenotype changes – Jacquiod et al. – Ecology Letters

Plastic mulch debris in rhizosphere: Interactions with soil-microbe-plant systems – Liu et al. – Science of The Total Environment

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

[PREPRINT]Urbanization promotes specific bacteria in freshwater microbiomes including potential pathogens – Numberger et al. – bioRxiv

Bioinformatics

[PREPRINT]specificity : an R package for generalized specificity analysis, with example analyses of Hawaiian foliar endophytic Fungi, human gut microbiome bacteria, and Antarctic glacier bacteria – Darcy et al. – bioRxiv

[PREPRINT]Unifying the known and unknown microbial coding sequence space – Vanni et al. – bioRxiv

Identifying prognostic pairwise relationships among bacterial species in microbiome studies – Devlin, Martin & Ostrovnaya – PLOS Computational Biology

HashSeq: a Simple, Scalable, and Conservative De Novo Variant Caller for 16S rRNA Gene Data Sets – Fouladi, Young & Fodor – mSystems

October 29, 2021

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Sorry for the delayed post, WordPress was playing some mean tricks on me today and there were no treats! Good morning all and happy spooky season! It’s been a moment since I’ve written a post and I write to you now as a freshly (pepper)minted PhD! I’m feeling gourd and can’t wait to pumpkin spice things up with some fangtastic papers.

Some of the highlights include a paper by McAlpine et al. examining interkingdom relationships between bacteria and fungi. Specifically, they found that the gut commensal species Lactobacillus can produce a small molecule that blocks filamentous growth of the opportunistic pathogen Candida albicans. Another interesting paper comes from Michael Adams lab at the University of Georgia, Athens which showed that members of the gut microbiota have the capacity to assimilate the metal tungsten which, in turn, allows these microbes to oxidize a broad range of aldehydes in the gut. Additionally, a paper by Plummer et al. looked at the vaginal microbiota of women who have recurrent bacterial vaginosis as well as the penile microbiota of their partners, and found that when males also underwent antibiotic treatment it led to a decrease in bacterial vaginosis in their female partners.

Hope you enjoy reading these fa-boo-lous papers and may you eat, drink, and be scary this Halloween!

General Microbiome
A small molecule produced by Lactobacillus species blocks Candida albicans filamentation by inhibiting a DYRK1-family kinase. – MacAlpine, J. et al., Nature Communications.

Pregnancy and Early-Life
Bifidobacterium species associated with breastfeeding produce aromatic lactic acids in the infant gut. – Laursen, M.F. et al., Nature Microbiology.

Bifidobacterium catabolism of human milk oligosaccharides overrides endogenous competitive exclusion driving colonization and protection. – Heiss, B.E. et al., Gut Microbes.

Mother’s Milk Microbiome Shaping Fecal and Skin Microbiota in Infants with Food Allergy and Atopic Dermatitis: A Pilot Analysis. – Gołębiewski. M. et al., Nutrients.

Early-life formula feeding is associated with infant gut microbiota alterations and an increased antibiotic resistance load. – Pärnänen, K.M.M. et al., The American Journal of Clinical Nutrition.

Human Vaginal Microbiome
A Prospective, Open-Label Pilot Study of Concurrent Male Partner Treatment for Bacterial Vaginosis. – Plummer, E.L. et al., mBio.

Human Gut Microbiome
Tungsten enzymes play a role in detoxifying food and antimicrobial aldehydes in the human gut microbiome. – Schut, G.J. et al., PNAS.

Commensal bacteria promote endocrine resistance in prostate cancer through androgen biosynthesis. – Pernigoni, N. et al., Science.

Vertebrate host phylogeny influences gut archaeal diversity. – Youngblut, N.D. et al., Nature Microbiology.

Gut microbiota dysbiosis contributes to the development of chronic obstructive pulmonary disease. – Li, N. et al., Respiratory Research.

Oral Administration of Latilactobacillus sakei ADM14 Improves Lipid Metabolism and Fecal Microbiota Profile Associated With Metabolic Dysfunction in a High-Fat Diet Mouse Model. – Won, S.-M. et al., Frontiers in Microbiology.

Human Oral Microbiome
Discrimination of Bacterial Community Structures among Healthy, Gingivitis, and Periodontitis Statuses through Integrated Metatranscriptomic and Network Analyses. – Nemoto, T. et al., mSystems.

Animal Experiments
Commensal segmented filamentous bacteria-derived retinoic acid primes host defense to intestinal infection. – Woo, V. et al., Cell Host & Microbe.

Intestinal microbiota shapes gut physiology and regulates enteric neurons and glia. – Vicentini, F.A. et al., Microbiome.

Lactobacillus rhamnosus GG Derived Extracellular Vesicles Modulate Gut Microbiota and Attenuate Inflammatory in DSS-Induced Colitis Mice. – Tong, L. et al., Nutrients.

Animal Microbiome
Phage Treatment Trial to Eradicate LA-MRSA from Healthy Carrier Pigs. – Tuomala, H. et al., Viruses.

Characterization of the Eukaryotic Virome of Mice from Different Sources. – Zhang, C. et al., Microorganisms.

Supplemental L-Arginine Improves the Embryonic Intestine Development and Microbial Succession in a Chick Embryo Model. – Dai, D. et al., Frontiers in Nutrition.

Water and Extremophile Microbiome
Plastic-Degrading Potential across the Global Microbiome Correlates with Recent Pollution Trends. – Zrimec, J. et al., mBio.

Acrylate protects a marine bacterium from grazing by a ciliate predator. – Teng, Z.-J. et al., Nature Microbiology.

Plant, Root, and Soil Microbiome
The fungal root endophyte Serendipita vermifera displays inter-kingdom synergistic beneficial effects with the microbiota in Arabidopsis thaliana and barley. – Mahdi, L.K. et al., ISME Journal.

Spatial Characterization of Microbial Communities on Multi-Species Leafy Greens Grown Simultaneously in the Vegetable Production Systems on the International Space Station. – Hummerick, M.E. et al., Life (Basel).

Relationships between community composition, productivity and invasion resistance in semi-natural bacterial microcosms. – Jones, M.L. et al., Elife.

Probiotics
High-efficiency delivery of CRISPR-Cas9 by engineered probiotics enables precise microbiome editing. – Neil, K. et al., Molecular Systems Biology.

Techniques
Visualizing transfer of microbial biomolecules by outer membrane vesicles in microbe-host-communication in vivo. – Bittel, M. et al., Journal of Extracellular Vesicles.

October 22, 2021

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Happy Friday!

Today’s digest includes an article on the role of age in the human intestinal microbiome, research on the role of a novel Acidobacteriota in seafloor sulfur cycling, work demonstrating the use of machine learning to predict camplyobacter source data, and much more! I also included the link to a page on “The Secret World Inside You”, a science exhibit focused on the human microbiome that is at the Witte Museum in San Antonio, Texas from now until April 10, 2022. If anyone ends up checking it out, I’d love to hear about it!

Events

A microbiome science exhibit, “The Secret World Inside You,” is at The Witte Museum in San Antonio, Texas from October 16, 2021 to April 10, 2022 .

Human gut microbiome

Bile acid-independent protection against Clostridioides difficile infection – Aguirre et al. – PLOS PATHOGENS

The importance of age in compositional and functional profiling of the human intestinal microbiome – Herzog et al. – PLOS ONE

Plant, root, and soil microbiome

The chosen few—variations in common and rare soil bacteria across biomes – Bickel & Or – The ISME Journal

The fungus Kalmusia longispora is able to cause vascular necrosis on Vitis vinifera – Karácsony et al. – PLOS ONE

Water and extremophile microbiome

Novel taxa of Acidobacteriota implicated in seafloor sulfur cycling – Flieder et al. – The ISME Journal

Beach sand oil spills select for generalist microbial populations – Heritier-Robbins et al. – The ISME Journal

Preprint: Influence of DNA extraction kits on the fungal DNA metabarcoding for freshwater environmental DNA – Matsuoka et al. – bioRxiv

Marine signature taxa and core microbial community stability along latitudinal and vertical gradients in sediments of the deepest freshwater lake – Reboul et al. – The ISME Journal

Phages and viruses

Review: Community context matters for bacteria-phage ecology and evolution – Blazanin & Turner – The ISME Journal

Bioinformatics

Machine learning to predict the source of campylobacteriosis using whole genome data – Arning et al. – PLOS GENETICS

October 20, 2021

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General microbiome

[REVIEW]Controlled Complexity: Optimized Systems to Study the Role of the Gut Microbiome in Host Physiology – Glowacki, Engelhart & Ahern – Frontiers in Microbiology

[REVIEW]Microbiota-brain interactions: Moving toward mechanisms in model organisms – Nagpal & Cryan – Neuron

Functional attractors in microbial community assembly – Estrela et al. – Cell Systems

Bloodstream infections’ origins following fecal microbiota transplantation: a strain- level analysis – Eshel et al. – Blood Advances

Probiotic consumption influences universal adaptive mutations in indigenous human and mouse gut microbiota – Ma et al. – Communications Biology

Multi-site human microbiome

[PREPRINT]Obesity influences composition of salivary and fecal microbiota and impacts the interactions between bacterial taxa – Bombin et al. – bioRxiv

Human vaginal microbiome

Does probiotics work for bacterial vaginosis and vulvovaginal candidiasis – Han & Ren – Current Opinion in Pharmacology

Human gut microbiome

A meta-analysis study of the robustness and universality of gut microbiome-metabolome associations – Muller, Algavi & Borenstein – Microbiome

Specific gut microbiome signatures and the associated pro-inflamatory functions are linked to pediatric allergy and acquisition of immune tolerance – de Filippis et al. – Nature Communications

Drinking Water Source and Intake Are Associated with Distinct Gut Microbiota Signatures in US and UK Populations – Vanhaecke et al. – The Journal of Nutrition

The Gut Microbiota during a Behavioral Weight Loss Intervention – Stanislawski et al. – Nutrients

Effect of chewing betel nut on the gut microbiota of Hainanese – Ying et al. – PLOS One

[PREPRINT]Codiversification of gut microbiota with humans – Suzuki et al. – bioRxiv

Response to PD-1-Based Immunotherapy for Non-Small Cell Lung Cancer Altered by Gut Microbiota – He et al. – Oncology and Therapy

Human metabolome

Changes in serum and urinary metabolomic profile after a dietary intervention in patients with irritable bowel syndrome – Nybacka et al. – PLOS One

The influence of the gut microbiome on BCG-induced trained immunity – Strazar et al. – Genome Biology

Animal microbiome

Weaning age and its effect on the development of the swine gut microbiome and resistome – Holman et at. – bioRxiv

Sandalwood seed oil improves insulin sensitivity in high-fat/high-sucrose diet-fed rats associated with altered intestinal microbiota and its metabolites – Gao et al. – Food & Function

Plant, root, and soil microbiome

Active virus-host interactions at sub-freezing temperatures in Arctic peat soil – Trubl et al. – Microbiome

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

PREPRINT[]Bacterial, phytoplankton, and viral dynamics of meromictic Lake Cadagno offer insights into the Proterozoic ocean microbial loop – Saini et al. – bioRxiv

Metagenomic analysis provides functional insights into seasonal change of a non-cyanobacterial prokaryotic community in temperate coastal waters – Matsumoto et al. – PLOS One

[PREPRINT]Survival of hatchery grown native oysters is associated with specific gut-associated bacteria at various locations within the Puget Sound – Kunselmann et al. – bioRxiv

Built environment (subways, indoor surfaces)

Microbial colonization and resistome dynamics in food processing environments of a newly opened pork cutting industry during 1.5 years of activity – Cobo-Diaz et al. – Microbiome

Food microbiology

Effects of ultrasound treatments on wine microorganisms – Munoz et al. – Ultrasonics Sonochemistry

Effect of roasting conditions on cocoa bioactivity and gut microbiota modulation – Maldonado-Mateus et al. – Food & Function

Bioinformatics

[PREPRINT]Development of a metatranscriptomic analysis method for multiple intestinal sites and its application to the common marmoset intestine – Uehara et al. – bioRxiv

Recovery of strain-resolved genomes from human microbiome through an integration framework of single-cell genomics and metagenomics – Arikawa et al. – Microbiome

[PREPRINT]Metagenome assembly of high-fidelity long reads with hifiasm-meta – Feng et al. – arXiv.org

Fast and Accurate Distance-based Phylogenetic Placement using Divide and Conquer – Balaban et al. – Molecular Ecology Resources

Microbes in the news (popular press, EurekAlert, ScienceDaily, Youtube, NPR, etc)

Should You Get a Microbiome Test? – Anahad O’Connor – New York Times

October 12th, 2021

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Bonjour from Paris, France ! Today’s digest contains a selection of really interesting preprints and published studies. In their review, Heilbronner and collaborators explore the role of bacteriocins, small antibacterial molecules produced by many commensal bacteria in human-associated microbiomes. The role of the bacteriocins in the human microbiome is of particular importance since they could be leveraged to specifically target colonizing pathogens while sparing mutualistic patners.

If you are interested in exploring new bioinformatic methods, I recommend taking a look at the study from Cheng and collaborators, who applied a novel iterative random forest approach to explore marine microbiome during algal blooms. They show how this model allow to identify conditions that are important causal factors of algal bloom dynamics.

Today’s non-microbiology pick is an opinion piece reflecting on the possible methods to develop the field of computational biology, ensure proper training and career development in this discipline and allow a greater collaboration between domain biologist and data scientists in multidisciplinary teams.

Have a great Tuesday!

Events and jobs

Virtual conference: Harnessing the plant microbiome – October 22-24, 2021
University of California, Davis, USA

Virtual conference: Reshaping the Microbiome through nutrition – November 17-19, 2021

General microbiome

Review: The microbiome-shaping roles of bacteriocins – Heilbronner et al. – Nature Reviews Microbiology

Human gut microbiome

Preprint: Gut Bacterial Dysbiosis and Instability is Associated with the Onset of Complications and Mortality in COVID-19 – Schult et al. – BioRXiv

Review: Nurturing the Early Life Gut Microbiome and Immune Maturation for Long Term Health – Dogra et al. – microorganisms

Animal experiments

Preprint: Mice with a humanized immune system are resilient to transplantation of human microbiota – Zhou et al. – BioRXiv

Animal microbiome

Preprint: Inter-species microbiota transplantation recapitulates microbial acquisition and persistence in mosquitoes – Coon et al. – BioRXiv

Water and extremophile microbiome

A novel random forest approach to revealing interactions and controls on chlorophyll concentration and bacterial communities during coastal phytoplankton blooms – Cheng et al. – Scientific reports

Built environment

Successional dynamics and alternative stable states in a saline activated sludge microbial community over 9 years – Wang et al. – Microbiome

Phages and viruses

Preprint: A Snapshot of the Global Drinking Water Virome: Diversity and Metabolic Potential Vary with Residual Disinfectant Use – Hegarty et al. – BioRXiv

Bioinformatics

Preprint: SynTracker: a synteny based tool for tracking microbial strains – Enav and Ley – BioRXiv

My non-microbiology pick

A field guide to cultivating computational biology – Way et al – PLOS biology

September 30, 2021

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Today’s digest includes a quantification of bacterial strains after fecal microbiota transplantation, a network analysis of the strawberry greenhouse soil microbiome after soil amendments, and an article about enhanced copper-resistance genes in Alteromonas macleodii. Also included are multiple preprints on topics such as denitrification pathways present in tunda soil metagenomes as well as the response of Endozoicomonas, a core coral bacterial group, to heat stress and host lysates.

General microbiome

Genomic population structure associated with repeated escape of Salmonella enterica ATCC14028s from the laboratory into nature – Achtman et al. – PLOS Genetics

Preprint: Role of the mobilome in the global dissemination of the carbapenem resistance gene blaNDM – Acman et al. – bioRxiv

Preprint: Existence of log-phase Escherichia coli persisters and lasting memory of a starvation pulse – Svenningsen et al. – bioRxiv

Human gut microbiome

Precise quantification of bacterial strains after fecal microbiota transplantation delineates long-term engraftment and explains outcomes – Aggarwala et al. – Nature Microbiology

Animal microbiome

A role for arthropods as vectors of multidrug-resistant Enterobacterales in surgical site infections from South Asia – Hassan et al. – Nature Microbiology

Plant, root, and soil microbiome

Response of soil microbiome structure and its network profiles to four soil amendments in monocropping strawberry greenhouse – Liu et al. – PLOS One

Preprint: Truncated denitrifiers dominate the denitrification pathway in tundra soil metagenomes – Pessi et al. – bioRxiv

Water and extremophile microbiome

Preprint: Response of Endozoicomonas montiporae to heat stress and coral host lysates – Chan et al. – bioRxiv

Enhanced copper-resistance gene repertoire in Alteromonas macleodii strains isolated from copper-treated marine coatings – Cusick et al. – PLOS One

Bacterial community structure of early-stage biofilms is dictated by temporal succession rather than substrate types in the southern coastal seawater of India – Sushmitha et al. – PLOS One

Preprint: Ecological stochasticity and phage induction diversify bacterioplankton communities at the microscale – Szabo et al. – bioRxiv

September 28, 2021

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Retraction Note

Retraction Note: IspH inhibitors kill Gram-negative bacteria and mobilize immune clearance – Singh et al. – Nature

Human oral microbiome

Oral Microbiota Profile of Individuals Who Abuse Methamphetamine – Yang et al. – Frontiers in Cellular and Infection Microbiology

The baseline oral microbiota predicts the response of locally advanced oral squamous cell carcinoma patients to induction chemotherapy: A prospective longitudinal study – Rui et al. – Radiotherapy and Oncology

Human gut microbiome

Gut microbiome in people living with HIV is associated with impaired thiamine and folate syntheses – Park et al. – Microbial Pathogenesis

[REVIEW]The impact of pelvic radiotherapy on the gut microbiome and its role in radiation-induced diarrhoea: a systematic review – Wang et al. – BMC Radiation Oncology

[REVIEW]Gut Microbiota-Mediated Modulation of Cancer Progression and Therapy Efficacy – Cheng et al. – Frontiers in Cell and Developmental Biology

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

Xylanase impact beyond performance: A microbiome approach in laying hens – van Hoeck et al. – PLOS One

Dysbiosis of the gut microbiome impairs mouse skeletal muscle adaptation to exercise – Valentino et al. – The Journal of Physiology

Lactic Acid Bacteria Strains Differently Modulate Gut Microbiota and Metabolic and Immunological Parameters in High-Fat Diet-Fed Mice – Fabersani et al. – Frontiers in Nutrition

Animal microbiome (for animals in the wild)

Alteration of Gut Microbiota of a Food-Storing Hibernator, Siberian Chipmunk Tamias sibiricus – Zhou, Wang & Yi – Microbial Ecology

[PREPRINT]Bacterial community dynamics during embryonic development of the little skate (Leucoraja erinacea) – Mika et al. – bioRxiv

Multi-omics reveals the positive leverage of plant secondary metabolites on the gut microbiota in a non-model mammal – Wang et al. – Microbiome

Plant, root, and soil microbiome

Trophic level drives the host microbiome of soil invertebrates at a continental scale – Zhu et al. – Microbiome

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

Genomic signatures of Lake Erie bacteria suggest interaction in the Microcystis phycosphere – Hoke et al. – PLOS One

Microbial river-to-sea continuum: gradients in benthic and planktonic diversity, osmoregulation and nutrient cycling – Tee et al. – Microbiome

Response and oil degradation activities of a northeast Atlantic bacterial community to biogenic and synthetic surfactants – Nikolova et al. – Microbiome

Built environment (subways, indoor surfaces)

The short-term effect of residential home energy retrofits on indoor air quality and microbial exposure: A case-control study – Nguyen, Holmes & Angenent – PLOS One

September 10, 2021

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In today’s digest read about a discovery of new Bordetella bronchiseptica-specific temperate and highly abundant siphoviruses that lead to the creation of a new genus Vojvodinavirus, biases in public human microbiome data, infant gut strain persistence, and more. Also, check out a list of upcoming microbiome events. Happy Friday!

Global microbiome

*Public human microbiome data dominated by highly developed countries – Richard J. Abdill – bioRxiv

Gut microbiome

Chinese gut microbiota and its associations with staple food type, ethnicity, and urbanization – Jing Lu – npj Biofilms and Microbiomes

Gut microbiota alterations in response to sleep length among African-origin adults – Na Fei – PlosOne

Bioaccumulation of therapeutic drugs by human gut bacteria – Martina Klünemann – Nature

*Infant gut strain persistence is associated with maternal origin, phylogeny, and traits including surface adhesion and iron acquisition – Yue Clare Lou – Cell Reports Medicine

Skin microbiome

Cotton and Surgical Face Masks in Community Settings: Bacterial Contamination and Face Mask Hygiene – Lize Delanghe – Frontiers in Medicine

Animal microbiome

The fall and rise of group B Streptococcus in dairy cattle: reintroduction due to human-to-cattle host jumps? – Chiara Crestani – Microbial Genomics

Viruses and phages

*Are Bordetella bronchiseptica Siphoviruses (Genus Vojvodinavirus) Appropriate for Phage Therapy—Bacterial Allies or Foes? – Aleksandra Petrovic Fabijan – Viruses

Water microbiome

Functional Redundancy in Ocean Microbiomes Controls Trait Stability – Taylor M. Royalty and Andrew D. Steen – bioRxiv

Bioinformatics

SHOOT: phylogenetic gene search and ortholog inference – David Emms and Steven Kelly – bioRxiv

Ultra-resolution Metagenomics: When Enough Is Not Enough – Falk Hildebrand – mSystems

Computational challenges and opportunities in spatially resolved transcriptomic data analysis – Lyla Atta & Jean Fan – Nature Communications

*BEEM-Static: Accurate inference of ecological interactions from cross-sectional microbiome data – Chenhao Li – Plos Computational Biology

Webinars &c

Conference: Microbiome Virtual International Conference #MVIF – September 14/16 (Atlantic/Pacific)

Course + Symposium: 2021 ISB Virtual Microbiome Series – October 13-15

Webinar: EMBARK Fall Webinars – a webinar series where invited speakers will be presenting their AMR research and be contrasted to EMBARK members presenting the work performed in the project.

For more, check out a collection of microbiome events HERE!

August 22nd, 2021

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Hyvää Päivää from Helsinki, Finland ! Today’s digest contains a selection of really interesting preprints and published studies. If you are interested in soil microbiology, take a look at the preprint by Nelson and collaborators, who characterized the soil microbiome across a wildfire burn severity gradients in coniferous forests and made their dataset available in the Fire Responding Ecogenomic database (FiRE-db).

Looking at a large variety of ecosystems, Rodriguez-Gijon and collaborators used a vast collection of Metagenomes Assembled Genomes (MAGs), to investigate the genomes size of prokaryotes in these ecosystems. They show that, while the environment of origin can be linked to genome size, it seems like evolutionary phylogenetic history is in many cases a stronger predictor.

Finally, today’s non-microbiology pick is a great “10 simples rules” paper reviewing best practices on organizing bioinformatics workshops in low and middle-income countries.

Have a great Weekend!

General microbiome

Preprint: A genomic perspective across Earth’s microbiomes reveals that genome size in Archaea and Bacteria is linked to ecosystem type and trophic strategy – Rodriguez-Gijon et al. – BioRXiV

Multi-site human microbiome

Review : Host-Microbe Metagenomics: a Lens To Refocus Our Perspective
on Infectious and Inflammatory Diseases – Kalantar and Langelier – mSystems

Human gut microbiome

Rectal bacteriome and virome signatures and clinical outcomes in community-acquired pneumonia: An exploratory study – Kullberg et al. – EClinicalMedicine

Review: The important role of fungi in inflammatory bowel diseases – Wang et al. – Scandinavian Journal of Gastroenterology

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

Preprint: A bacterial genome and culture collection of gut microbial in weanling piglet – Dong et al. – BioRXiV

Characterization of the fecal microbiota of sows and their offspring from German commercial pig farms – Lührmann et al. – Plos One

Plant, root, and soil microbiome

Preprint: Does plant diversity determine the diversity of the rhizosphere microbial community? – Zverev et al. – BioRXiV

Preprint: Playing with FiRE: A genome resolved view of the soil microbiome responses to high severity forest wildfire – Nelson et al. – BioRXiV

Peatland microbial community responses to plant functional group and drought are depth-dependent – Lamit et al. – Molecular ecology

Soil pH determines bacterial distribution and assembly processes in natural mountain forests of eastern China – Ni et al. – Global ecology and Biogeography

Water and extremophile microbiome

Preprint: The OceanDNA MAG catalog contains over 50,000 prokaryotic genomes originated from various marine environments – Nishimura et al. – BioRXiV

Food microbiology

Preprint: Mixed culture metagenomics of the microbes making sour beer – Piraine et al. – BioRXiV

Preprint: Insights into the nutritional properties and microbiome diversity in sweet and sour yogurt manufactured in Bangladesh – Tanzina et al. – BioRXiV

Preprint: Microbial communities in retail draft beers and the biofilms they produce – Bose et al. – BioRXiV

Bioinformatics

Book chapter: Bioinformatics Tools and Software – Gupta et al. – Advances in Bioinformatics, Springer, Singapore

MiDSystem: A comprehensive online system for de novo assembly and analysis of microbial genomes – Lee et al. – New biotechnology

My non-microbiology picks

Ten simple rules for organizing a bioinformatics training course in low– and middle-income countries – Moore et al. – PLOS computational biology