Monthly Archives: October 2021

October 29, 2021

Posted on by

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

Posted on by

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 24, 2021

Posted on by

Highlights!

Intestinal Bacteriophage Therapy: Looking for Optimal Efficacy – François Javaudin – Clinical Microbiology Reviews → in this review, authors discuss different aspects of the applications of bacteriophage therapy in mammals.

Wildlife symbiotic bacteria are indicators of the health status of the host and its ecosystem – Maria Bravo – Applied and Environmental Microbiology → This study highlights the role of lactic acid bacteria as an useful indicator of wildlife health status. 

High-coverage metabolomics uncovers microbiota-driven biochemical landscape of interorgan transport and gut-brain communication in mice – Yunjia Lai – Nature Communications → in this report, profile from stool, blood and brain samples were obtained comparing germ-free and conventional mice, in order to gain more insight about the microbiota-gut-brain axis.

Human and General Microbiome

Analysis of gut microbiota and metabolites in patients with rheumatoid arthritis and identification of potential biomarkers – Yumei Chen – Aging

Gut-microbiota-microglia-brain interactions in Alzheimer’s disease: knowledge-based, multi-dimensional characterization – QuanQiu Wang – Alzheimer’s Research & Therapy

Alterations in the oral microbiome in HIV infection: causes, effects and potential interventions – Shuang Li – Chinese Medical Journal

Utilization efficiency of human milk oligosaccharides by human-associated Akkermansia is strain-dependent – Estefani Luna – Applied and Environmental Microbiology

Upper Respiratory Tract Microbiome of Australian Aboriginal and Torres Strait Islander Children in Ear and Nose Health and Disease – Andrea Coleman – Microbiology Spectrum

Review: The Human Microbiome in immunobullous disorders and lichen planus – M Karimova – Clinical and Experimental Dermatology

Beneficial Microbes and Compounds

Review: What is unknown in using Microbiota as a Therapeutic? – Joseph Jy Sung – Journal of Gastroenterology and Hepatology

Isolation and Identification of Potential Probiotic Bacteria from Human Milk – Quésia S Damaceno – Probiotics and Antimicrobial Proteins

Probiotics as the live microscopic fighters against Helicobacter pylori gastric infections – Masoud Keikha – BMC Gastroenterology

The probiotic Companilactobacillus crustorum MN047 alleviates colitis-associated tumorigenesis via modulating the intestinal microenvironment – Tao Wang – Food & Function

Lactobacillus rhamnosus and Bifidobacterium longum alleviate colitis and cognitive impairment in mice by regulating IFN-γ to IL-10 and TNF-α to IL-10 expression ratios – Xiaoyang Ma – Scientific Reports

Review: Interaction between four galactans with different structural characteristics and gut microbiota – Song Li – Critical Reviews in Food Science and Nutrition

Non-Model Animal Microbiome

Habitat Disturbance Linked with Host Microbiome Dispersion and Bd Dynamics in Temperate Amphibians – Wesley J Neely – Microbial Ecology

The Microbial Composition of Penaeid Shrimps’ Hepatopancreas Is Modulated by Hemocyanin – Zhihong Zheng – Journal of Immunology

Overabundance of Asaia and Serratia Bacteria Is Associated with Deltamethrin Insecticide Susceptibility in Anopheles coluzzii from Agboville, Côte d’Ivoire – Bethanie Pelloquin – Microbiology Spectrum

Genomics and phylogeny of the proposed phylum ‘Candidatus Poribacteria’ associated with the excavating sponge Thoosa mismalolli – Adrián González-Castillo – Antonie van Leeuwenhoek

Plant Microbiome

Microbial Diversity in Cultivated and Feral Vanilla Vanilla planifolia Orchids Affected by Stem and Rot Disease – Ireri A Carbajal-Valenzuela – Microbial Ecology

Indirect reduction of Ralstonia solanacearum via pathogen helper inhibition – Mei Li – The ISME Journal

Comparative Analysis of the Cultured and Total Bacterial Community in the Wheat Rhizosphere Microbiome Using Culture-Dependent and Culture-Independent Approaches – Sameh H Youseif – Microbiology Spectrum

Other Microbes

Mechanistic Insight into Yeast Bloom in a Lactic Acid Bacteria Relaying-Community in the Start of Sourdough Microbiota Evolution – Mugihito Oshiro – Microbiology Spectrum

October 22, 2021

Posted on by

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

Posted on by

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 16, 2021

Posted on by

Highlights!

Parallelism of intestinal secretory IgA shapes functional microbial fitness – Tim Rollenske – Nature → By using recombinant IgAs, researchers showed that IgA may shape the metabolism of intestinal bacteria, and in some cases IgA molecules against a same target have a different effect on the activity.

Hallstatt miners consumed blue cheese and beer during the Iron Age and retained a non-Westernized gut microbiome until the Baroque period – Frank Maixner – Current Biology → From the analysis of paleofeces, researchers suggest that people from the Austrian zone of Hallstatt could retain a non-westernized diet for centuries; in some cases, a high consumption of blue cheese and beer is suggested by the detection of Penicillium roqueforti and Saccharomyces cerevisiae DNA in the samples.  

In vitro study of the effect of quinoa and quinoa polysaccharides on human gut microbiota – Hitache Zeyneb – Food Science & Nutrition → quinoa, a very nutritious Andean cereal,  contains polysaccharides with potential prebiotic (health-promoting) properties.

Metagenomic analysis of gut microbiome reveals a dynamic change in Alistipes onderdonkii in the preclinical model of pancreatic cancer, suppressing its  proliferation – Kihak Lee – Applied Genetics and Molecular Biotechnology → RNA-seq analysis in a preclinical model revealed that the A. onderdonkii medium induced unique transcriptomic alterations in the pancreatic cancer cells, suggesting an special role in this disease.

Human and General Microbiome

Review: Biomarkers of geroprotection and cardiovascular health: An overview of omics studies and established clinical biomarkers in the context of diet – Riccardo Secci – Critical Reviews in Food Science and Nutrition

Unravelling the collateral damage of antibiotics on gut bacteria – Lisa Maier – Nature

Direct on-swab metabolic profiling of vaginal microbiome host interactions during pregnancy and preterm birth – Pamela Pruski – Nature Communications

Brain development in premature infants: A bug in the programming system? – Gerard Clarke – Cell Host & Microbe

A colon cancer prequel – John T Wren – Cell Host & Microbe

Metagenomic Analysis of Saliva Reveals Disease-Associated Microbiotas in Patients With Periodontitis and Crohn’s Disease-Associated Periodontitis – Boyang Sun – Frontiers in Cellular and Infection Microbiology

Antibiotic use but not gastrointestinal infection frequently precedes first diagnosis of functional gastrointestinal disorders – Michael P Jones – United European Gastroenterology Journal

Impact of Helicobacter pylori eradication on the gastric microbiome – Li-Qi Mao – Gut Pathogens

Baseline co-medications may alter the anti-tumoural effect of checkpoint inhibitors as well as the risk of immune-related adverse events – Marie Kostine – European Journal of Cancer

Cultivation of common bacterial species and strains from human skin, oral, and gut microbiota – Elizabeth Fleming – BMC Microbiology

Effect of chewing betel nut on the gut microbiota of Hainanese – Li Ying – PloS ONE

Animal Models

Transplantation of fecal microbiota from patients with inflammatory bowel disease and depression alters immune response and behavior in recipient mice – Hyo-Min Jang – Scientific Reports

Temporal relationship between alterations in the gut microbiome and the development of polycystic ovary syndrome-like phenotypes in prenatally androgenized female mice – Akari Kusamoto – The FASEB Journal

Gut microbiota dysbiosis of type 2 diabetic mice impairs the intestinal daily rhythms of GLP-1 sensitivity – Estelle Grasset – Acta Diabetologica

Non-Model Animal Microbiome

Diurnal oscillations in gut bacterial load and composition eclipse seasonal and lifetime dynamics in wild meerkats – Alice Risely – Nature Communications

Diet diversity and environment determine the intestinal microbiome and bacterial pathogen load of fire salamanders – Yu Wang – Scientific Reports

The structure of the cereal leaf beetle (Oulema melanopus) microbiome depends on the insect’s developmental stage, host plant, and origin – Beata Wielkopolan – Scientific Reports

Beneficial Microbes and Compounds

Review: Does probiotics work for bacterial vaginosis and vulvovaginal candidiasis – Yue Han – Current Opinion in Pharmacology

Characterization of a new bacteriocin-like inhibitory peptide produced by Lactobacillus sakei B-RKM 0559 – Gulyaim K Abitayeva – Biotechnology Letters

Probiotic Interventions Alleviate Food Allergy Symptoms Correlated With Cesarean Section: A Murine Model – Bi-Ying Jin – Frontiers in Immunology

Selenium-enriched Bifidobacterium longum DD98 attenuates irinotecan-induced intestinal and hepatic toxicity in vitro and in vivo – Hui Zhu – Biomedicine & Pharmacotherapy

Phages

Novel lytic bacteriophage vB_GEC_EfS_9 against Enterococcus faecium – S Rigvava – Virus Research

Environmental Microbiome

Charting the complexity of the activated sludge microbiome through a hybrid sequencing strategy – Lei Liu – Microbiome

Other

PBK model-based prediction of intestinal microbial and host metabolism of zearalenone and consequences for its estrogenicity – Diana M Mendez-Catala – Molecular Nutrition & Food Research

October 12th, 2021

Posted on by

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 9, 2021

Posted on by

Highlights!

Commensal microbiota divergently affect myeloid subsets in the mammalian central nervous system during homeostasis and disease – Roman Sankowski – The EMBO Journal → This study shows how perturbations in the microbiota drive changes in gene expression profiles in the CNS-associated macrophages, with concomitant effects on the  CNS myeloid cells, including Alzheimer-associated repercussions in a specialized murine model.

Coordination of root auxin with the fungus Piriformospora indica and bacterium Bacillus cereus enhances rice rhizosheath formation under soil drying – Feiyun Xu – The ISME Journal → In this study, authors report a cooperative effect of an endophytic fungus and a plant growth-promoting bacterium in rhizosheath formation when moderate soil drying, an agricultural technique used to improve water utilization, is performed.

Human and General Microbiome

Review: The role of Akkermansia muciniphila in obesity, diabetes and atherosclerosis – Alka Hasani – Journal of Medical Microbiology

Review: How can probiotic improve irritable bowel syndrome symptoms? – Indira Benjak Horvat – World Journal of Gastrointestinal Surgery

Meta-Analysis of the Composition of Human Intestinal Gases – Andre Modesto – Digestive Diseases and Sciences

Effectiveness of Probiotics and Prebiotics Against Acute Liver Injury: A Meta-Analysis – Sheng Xu – Frontiers in Medicine

The bacterial gut microbiome of probiotic-treated very-preterm infants: changes from admission to discharge – Jacob A F Westaway – Pediatric Research

Discovery of β-N-acetylglucosaminidases from screening metagenomic libraries and their use as thioglycoligase mutants – Gregor Tegl – Organic & Biomolecular Chemistry

Animal Microbiome

Comparing the gut microbiome along the gastrointestinal tract of three sympatric species of wild rodents – Jason L Anders – Scientific Reports

Changes in rumen microbial community composition in yak in response to seasonal variations – Xiaodan Huang – Journal of Applied Microbiology

Faecalicatena faecalis sp. nov., a moderately alkaliphilic bacterial strain isolated from swine faeces – Byeong Seob Oh – Antonie van Leeuwenhoek

Plant Microbiome

Capacity of soil bacteria to reach the phyllosphere and convergence of floral communities despite soil microbiota variation – Julien Massoni –  PNAS

Distinct Endophytic Bacterial Communities Inhabiting Seagrass Seeds – Flavia Tarquinio – Frontiers in Microbiology

Fungi Microbiome

Widespread bacterial diversity within the bacteriome of fungi – Aaron J Robinson – Communications Biology

Environmental Microbiome

Preprint: Genomic and metabolic adaptations of biofilms to ecological windows of opportunities in glacier-fed streams – Susheel Bhanu Busi – Biorxiv

October 8, 2021

Posted on by

Today’s digest features a metagenomic meta-study on faecal microbiota transplantation, RibDif for count and compare 16S rRNA genes within a genus, and more. Also, there is a new FEMS Microbiology Letters collection of articles highlighting the evolution of education during the COVID-19 pandemic.

There is still time to join in the second 🌎 Microbiome Virtual International Forum 🌏. Recordings from previous MVIF can be found here.

And, the #Microber2021 just started! Check out this microbe edition of #Inktober drawing challenge – during October, every day a new scientific art on microbiology topic.

Global microbiome

Cultivating Healthy Connections: Exploring and Engineering the Microbial Flow That Shapes Microbiomes – Travis J. Wiles – mSystems

Neonatal microbiome

Presence of distinctive microbiome in the first-pass meconium of newborn infants – Jenni Turunen – Scientific Reports

Respiratory microbiome

Divergence of bacterial communities in the lower airways of CF patients in early childhood – John B. O’Connor – PlosOne

Gut microbiome

Drivers and Determinants of Strain Dynamics Following Faecal Microbiota Transplantation – Thomas Schmidt – bioRxiv

Western and non-western gut microbiomes reveal new roles of Prevotella in carbohydrate metabolism and mouth–gut axis – Vishnu Prasoodanan P. K. – npj Biofilms and Microbiomes

Animal microbiome

Phylogenetic systematics of Butyrivibrio and Pseudobutyrivibrio genomes illustrate vast taxonomic diversity, open genomes and an abundance of carbohydrate-active enzyme family isoforms – Sara E. Pidcock – Microbial Genomics

Animal experiment

Metabolic modulation of tumours with engineered bacteria for immunotherapy – Fernando P. Canale – Nature

Citrobacter amalonaticus Inhibits the Growth of Citrobacter rodentium in the Gut Lumen – Caroline Mullineaux-Sanders – mBio

Regulation of blood–brain barrier integrity by microbiome-associated methylamines and cognition by trimethylamine N-oxide – Lesley Hoyles – bioRxiv

Effects of prebiotic oligofructose-enriched inulin on gut-derived uremic toxins and disease progression in rats with adenine-induced chronic kidney disease – Ebru Melekoglu – PlosOne

Plant microbiome

Prevalence and Specificity of Chemoreceptor Profiles in Plant-Associated Bacteria – Claudia Sanchis-López – mSystems

Food

Bacteriocinogenic lactic acid bacteria in the traditional cereal-based beverage Boza: a genomic and functional approach – Luciano Lopes Queiroz – bioRxiv

Bioinformatics

metaGEM: reconstruction of genome scale metabolic models directly from metagenomes – Francisco Zorrilla – Nucleic Acids Research

RibDif: can individual species be differentiated by 16S sequencing? – Mikael Lenz Strube – Bioinformatics Advances

eggNOG-mapper v2: Functional Annotation, Orthology Assignments, and Domain Prediction at the Metagenomic Scale – Carlos P Cantalapiedra – Molecular Biology and Evolution

Sequencing DNA with nanopores: Troubles and biases – Clara Delahaye and Jacques Nicolas – PlosOne

Webinars &c

Conference: Microbiome Virtual International Conference #MVIF – October 14 (Pacific Live)/15 (Atlantic Reply)

Webinar: EMBARK Fall Webinars – a webinar series focused on AMR research

Microscopy Live! – Geology – an hour of live electron microscopy, guided by the audience – Plymouth Electron Microscopy Centre (October 29)

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

Happy #Microber2021, sci-art October!

October 06, 2021

Posted on by

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