Category Archives: Animal experiments

November 26, 2021

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General microbiome

Metabolomics-Microbiome Crosstalk in the Breast Cancer Microenvironment – Al-Ansari – Metabolites

Aspergillus fumigatus pan-genome analysis identifies genetic variants associated with human infection – Barber et al. – Nature Microbiology

Human gut microbiome

Human gut bacterial metabolism drives Th17 activation and colitis – Alexander et al. – Cell Host & Microbiome

Integrative Analysis of Metabolome and Microbiome in Patients with Progressive Alcohol-Associated Liver Disease – Gao et al. – Metabolites

Human Fecal Metabolome Reflects Differences in Body Mass Index, Physical Fitness, and Blood Lipoproteins in Healthy Older Adults – Cui et al. – Metabolites

[REVIEW]Gut Microbiota, Microbial Metabolites and Human Physical Performance – Lensu & Pekkala – Metabolites

[Editorial]Next steps after 15 stimulating years of human gut microbiome research – Clavel et al. – Microbial Biotechnology

[REVIEW]The microbiome, Gastrointestinal cancer and immunotherapy – Newsome, Yang & Jobin – Journal of Gastroenterology and Hepatology

Mycobiota-induced IgA antibodies regulate fungal commensalism in the gut and are dysregulated in Crohn’s disease – Doron et al. – Nature Microbiology

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

Fecal microbiota transplantation protects rotenone-induced Parkinson’s disease mice via suppressing inflammation mediated by the lipopolysaccharide-TLR4 signaling pathway through the microbiota-gut-brain axis – Zhao et al. – Microbiome

Xylan alleviates dietary fiber deprivation-induced dysbiosis by selectively promoting Bifidobacterium pseudocatenulatum in pigs – Wang et al. Microbiome

Animal microbiome (for animals in the wild)

Circadian dynamics of the teleost skin immune-microbiome interface – Ellison, Wilcockson & Cable – Microbiome

Honey bee genetics shape the strain-level structure of gut microbiota in social transmission – Wu et al. – Microbiome

Plant, root, and soil microbiome

Evidence for host–microbiome co-evolution in apple – Abdelfattah et al. – New Phytologist

Protective role of the Arabidopsis leaf microbiota against a bacterial pathogen – Vogel et al. – Nature Microbiology

Emergent bacterial community properties induce enhanced drought tolerance in Arabidopsis – Yang et al. – npj Biofilms and Microbiomes

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

Cross-regional scale pollution of freshwater biofilms unveiled by antibiotic resistance genes – Yao et al. – Science of The Total Environment

Functional metagenomic analysis of quorum sensing signaling in a nitrifying community – Tan et al. – npj Biofilms and Microbiomes

Bioinformatics

Multivariable association discovery in population-scale meta-omics studies – Mallick et al. – PLOS Computational Biology

Techniques

Assessing saliva microbiome collection and processing methods – Armstrong, Parmar & Blaser – npj Biofilms and Microbiomes

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 27, 2021

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COVID19

Severe dysbiosis and specific Haemophilus and Neisseria signatures as hallmarks of the oropharyngeal microbiome in critically ill COVID-19 patients – de Castilhos et al – Clinical Infectious Diseases

General microbiome

The Role of Microbiota in Infant Health: From Early Life to Adulthood – Yao et al. – Front. Immunol.

The microbiome impacts host hybridization and speciation – Miller et al. – PLOS Biology

Pregnancy and early life

Gut Dysbiosis, Bacterial Colonization and Translocation, and Neonatal Sepsis in Very-Low-Birth-Weight Preterm Infants – Lee et al. – Front. Microbiol.

Multi-site human microbiome

Oral, nasal, and gut microbiota in Parkinson’s disease – Li et al. – Neuroscience

Human respiratory microbiome

[REVIEW]Emerging cellular and molecular interactions between the lung microbiota and lung diseases – Xiang & Meng – Critical Reviews in Microbiology

Human gut microbiome/mycobiome

[REVIEW]Drugs and Bugs: The Gut-Brain Axis and Substance Use Disorders – Simpson et al. – Journal of Neuroimmune Pharmacology

Metagenomic analysis reveals the signature of gut microbiota associated with human chronotypes – Carasso et al. – The FASEB Journal

Intestinal mycobiota composition and changes in children with thalassemia who underwent allogeneic hematopoietic stem cell transplantation – Yalcin et al. – Pediatric Blodd & Cancer

Gut microbiota analyses of Saudi populations for type 2 diabetes-related phenotypes reveals significant association – AlAli et al. – bioRxiv

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

Consistent gut bacterial and short-chain fatty acid signatures in hypoabsorptive bariatric surgeries correlate with metabolic benefits in rats – Mukorako et al. – International Journal of Obesity

Microbiota instruct IL-17A-producing innate lymphoid cells to promote skin inflammation in cutaneous leishmaniasis – Singh et al – PLOS Pathogens

Anti-inflammatory effects of purple sweet potato anthocyanin extract in DSS-induced colitis: modulation of commensal bacteria and attenuated bacterial intestinal infection – Mu et al. – Food & Function

Plant, root, and soil microbiome/virome

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

Arabidopsis assemble distinct root-associated microbiomes through the synthesis of an array of defense metabolites – Kudjordjie, Sapkota & Nicolaisen – PLOS One

Microbiome of Pukzing Cave in India shows high antimicrobial activity against plant and animal pathogens – Iquebal et al. – Genomics

[REVIEW]Phyllosphere microbiome: Diversity and functions – Bashir et al. – Microbiological Research

[REVIEW]Rhizospheric microbiome: Bio-based emerging strategies for sustainable agriculture development and future perspectives – Kumawat, Razdan & Saharan – Microbiological Research

Phages and viruses

[REVIEW]The intestinal virome: lessons from animal models – Chaffringeon et al. – Current Opinion in Virology

Bioinformatics

[REVIEW]Application of Deep Learning in Plant–Microbiota Association Analysis – Deng et al. – Frontiers in Genetics

Techniques

Simple solution to preserve plant samples for microbiome analyses – Carvalhais et al. – Molecular Ecology Resources

[REVIEW]Novel methods of microbiome analysis in the food industry – Sabater et al. – nternational Microbiology

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

October 06, 2021

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General microbiome

The intestinal 3M (microbiota, metabolism, metabolome) Zeitgeist – from fundamentals to future challenges – Dey et al. – Free Radical Biology and Medicine

Pregnancy and early life

Gut microbiota changes in preeclampsia, abnormal placental growth and healthy pregnant women – Huang et al. – BMC Microbiology

Human respiratory microbiome

Refinement of microbiota analysis of specimens from patients with respiratory infections using next-generation sequencing – Ikegami et al. – Scientific Reports

Human skin microbiome

Experimental Dermatology Special Issue with Focus on ‘Skin microbiome and antimicrobial peptides’

Human gut microbiome

[REVIEW]Gut microbiome in pediatric acute leukemia: from predisposition to cure – Masetti et al. – Blood Advances

Animal microbiome

Effects of moderate exercise on hepatic amino acid and fatty acid composition, liver transcriptome, and intestinal microbiota in channel catfish (Ictalurus punctatus) – Zhang et al. – Comparative Biochemistry and Physiology Part D: Genomics and Proteomics

Metagenomic Sequencing Reveals that High-Grain Feeding Alters the Composition and Metabolism of Cecal Microbiota and Induces Cecal Mucosal Injury in Sheep – Xie, Wang & Mao – mSystems

Plant, root, and soil microbiome

Biodegradable and conventional microplastics exhibit distinct microbiome, functionality, and metabolome changes in soil – Sun et al. – Journal of Hazardous Materials

Soil microbiota and microarthropod communities in oil contaminated sites in the European Subarctic – Melekhina et al. – Scientific Reports

Fast and persistent responses of alpine permafrost microbial communities to in situ warming – Perez-Mon et al. – Science of The Total Environment

Built environment (subways, indoor surfaces)

Environmental dynamics of hospital microbiome upon transfer from a major hospital to a new facility – Ashokan et al. – Journal of Infection

Bioinformatics

[Commentary]Predicting Microbiome Metabolism and Interactions through Integrating Multidisciplinary Principles – Schmidt, Ghadermazi & Chan – mSystems

Uniform Manifold Approximation and Projection (UMAP) Reveals Composite Patterns and Resolves Visualization Artifacts in Microbiome Data – Armstrong et al. – mSystems

October 5, 2021

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Today’s digest includes a description of how probiotics modulate B cells in Peyer’s patches published in Microbiome, a review in ISME on microbial storage in soil and multiple recent Cell Host & Microbe articles covering the plant immune system and colonisation resistance to Salmonella and Klebsiella.

General microbiome

Single-colony sequencing reveals microbe-by-microbiome phylosymbiosis between the cyanobacterium Microcystis and its associated bacteria – Pérez-Carrascal et al. Microbiome

Molecular basis of a bacterial-amphibian symbiosis revealed by comparative genomics, modeling, and functional testing – Brunetti et al. ISME

Human gut microbiome

Gut microbiota involved in leptospiral infections – Xie et al. ISME

Identification of Faecalibacterium prausnitzii strains for gut microbiome-based intervention in Alzheimer’s-type dementia – Ueda et al. Cell Reports Medicine

Fecal microbial transplantation and fiber supplementation in patients with severe obesity and metabolic syndrome: a randomized double-blind, placebo-controlled phase 2 trial – Mocanu et al. Nature Medicine

Gut bacteria identified in colorectal cancer patients promote tumourigenesis via butyrate secretion – Okumura et al. Nature Communications

E. coli enhance colonization resistance against Salmonella Typhimurium by competing for galactitol, a context-dependent limiting carbon source – Eberl et al. Cell Host & Microbe

Klebsiella oxytoca causes colonization resistance against multidrug-resistant K. pneumoniae in the gut via cooperative carbohydrate competition – Osbelt et al. Cell Host & Microbe

Human Oral Microbiome

Distinct B cell subsets in Peyer’s patches convey probiotic effects by Limosilactobacillus reuteri – Liu et al. Microbiome

Human Oral Microbiome

Metagenomic analysis of ancient dental calculus reveals unexplored diversity of oral archaeal Methanobrevibacter – Granehäll et al. Microbiome

Soil & Plant microbiomes

[REVIEW] Microbial storage and its implications for soil ecology – Mason-Jones et al. ISME

Gammaproteobacteria, a core taxon in the guts of soil fauna, are potential responders to environmental concentrations of soil pollutants – Zhang et al. Microbiome

Plant immune system activation is necessary for efficient root colonization by auxin-secreting beneficial bacteria – Tzipilevich et al. Cell Host & Microbe

October 1, 2021

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Multi-site human microbiome

Diagnostic and prognostic potential of the oral and gut microbiome for lung adenocarcinoma – Lim et al. – Clinical and Translational Medicine

Human oral microbiome

Individuals with substance use disorders have a distinct oral microbiome pattern – Kosciolek et al. – Brain, Behavior, & Immunity – Health

Human skin microbiome

[REVIEW]The Dynamics of Skin Microbiota in Shoulder Surgery Infections – Fatima, Bjarnsholt & Bay – Journal of Pathology, Microbiology and Immunology

Human gut microbiome

[REVIEW]Mucins, gut microbiota, and postbiotics role in colorectal cancer – Pothuraju et al. – Gut Microbes

Age and the aging process significantly alter the small bowel microbiome – Leite et al. – Cell Reports

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

Guidelines for reporting on animal fecal transplantation (GRAFT) studies: recommendations from a systematic review of murine transplantation protocols – Secombe et al. – Gut Microbes

Alpha-synuclein alters the faecal viromes of rats in a gut-initiated model of Parkinson’s disease – Stockdale et al. – Communications Biology

[PREPRINT]First trimester gut microbiome induces Inflammation-dependent gestational diabetes phenotype in mice – Pinto et al. – medRxiv

[PREPRINT]High-resolution genetic mapping of the mucosa-associated gut microbiome in hybrid mice provides novel insight on the impact of host genetics – Doms et al. – bioRxiv

Plant, root, and soil microbiome

Effects of microplastics on soil microbiome: The impacts of polymer type, shape, and concentration – Sun et al. – Science of the total Environment

Bioinformatics

Long-read metagenomics of multiple displacement amplified DNA of low-biomass human gut phageomes by SACRA preprocessing chimeric reads – Kiguchi et al. – DNA Research

BiG-MAP: an Automated Pipeline To Profile Metabolic Gene Cluster Abundance and Expression in Microbiomes – Andreu et al. – mSystems

Increasing the power of interpretation for soil metaproteomics data – Jouffret – Microbiome