December 02, 2020

General microbiome

The Interplay of Sex Steroids, the Immune Response, and the Intestinal Microbiota – Pace & Watnick – Trends in Microbiology

[REVIEW]Circulating 16S RNA in Biofluids: Extracellular Vesicles as Mirrors of Human Microbiome? – Ricci et al. – Int. J. Mol. Sci.

[REVIEW]Microbiota and Obesity: Where Are We Now? – Ballini et al. – Biology

Human vaginal microbiome

Vaginal Microbiome-Based Bacterial Signatures for Predicting the Severity of Cervical Intraepithelial Neoplasia – Lee et al. – Diagnostics

Human gut microbiome

A functional ecological network based on metaproteomics responses of individual gut microbiomes to resistant starches – Li et al. – Computational and Structural Biotechnology Journal

[REVIEW]Personalized Nutrition Through The Gut Microbiota: Current Insights And Future Perspectives – Vandeputte – Nutrion Reviews

[REVIEW]Harnessing the gut microbiota to promote metabolic health – Zmora – Nutrion Reviews

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

Cage bedding modifies metabolic and gut microbiota profiles in mouse studies applying dietary restriction – Gregor et al. – Scientific Reports

Animal microbiome (for animals in the wild)

Influence of Environmental Stressors on the Microbiota of Zebra Mussels (Dreissena polymorpha) – Mathai et al. – Invertebrate Microbiology

Gut microbiota protects honey bees (Apis mellifera L.) against polystyrene microplastics exposure risks – Wang et al. – Journal of Hazardous Materials

Plant, root, and soil microbiome

Variable characteristics of microbial communities on the surface of sweet cherries under different storage conditions – Zhang et al. – Postharvest Biology and Technology

Biodiversity of pesticides degrading microbial communities and their environmental impact – Kumar et al. – Biocatalysis and Agricultural Biotechnology

Bioinformatics

[REVIEW]Evaluating and minimizing batch effects in metabolomics – Han & Li – Mass Spectrometry Reviews

November 30, 2020

Hello from Luebeck! Today we selected among others maternal obesity and neurodevelopment, infant growth, breastfeeding and c-section, dental microbiome, gut microbiome and diseases/cancer, a couple of animal and plant microbiome studies. Of particular interest is a study diet and problem solving in a bird species (Parus major).

General microbiome

[REVIEW]The dynamic wound microbiome – Liu et al. – BMC Medicine

[REVIEW]Microbiome and Cervical Cancer – Castanheira et al. – Pathobiology

Pregnancy and early life

[REVIEW]The impact of maternal obesity on childhood neurodevelopment – Tong & Kalish – Journal of Perinatology

Perinatal environment shapes microbiota colonization and infant growth: impact on host response and intestinal function – Selma-Royo et al. – Microbiome

Breastfeeding restored the gut microbiota in caesarean section infants and lowered the infection risk in early life – Guo et al. BMC Pediatrics

Human oral microbiome

Dental plaque microbiota profiles of children with caries-free and caries-active dentition – Qudeimat et al. – Journal of Dentistry

[REVIEW]Microbiomics: Were we all wrong before? – Kumar – Periodontology 2000

[REVIEW]Metaproteome and metabolome of oral microbial communities – Bostanci et al. – Periodontology 2000

Human gut microbiome

Gutmicrobiota, immunity and pain – Santoni, Miccini & Batelli – Immunology Letters

The Healthy Microbiome (What is the definition of a healthy gut microbiome?) – Shanahan, Ghosh & O’Toole – Gastroenterology

Altered gut bacterial and metabolic signatures and their interaction in gestational diabetes mellitus – Wang et al. – Gut Microbes

Animal microbiome (for animals in the wild)

Diet induces parallel changes to the gut microbiota and problem solving performance in a wild bird – Davidson et al. Scientific Reports

Wild black bears harbor simple gut microbial communities with little difference between the jejunum and colon – Gillman, McKenney & Lafferty – Scientific Reports

Age Patterning in Wild Chimpanzee Gut Microbiota Diversity Reveals Differences from Humans in Early Life – Reese et al. – Current Biology

Plant, root, and soil microbiome

Genetic selection for growth drives differences in intestinal microbiota composition and parasite disease resistance in gilthead sea bream – Piazzon et al. – Microbiome

A comparison of the functional diversity of microbial communities in maize rhizosphere soils in the North West Province of South Africa – Chinenyenwa Fortune Chukwuneme, Ayansina Segun Ayangbenro, Olubukola Oluranti Babalola – Rhizosphere

[REVIEW]Beyond the extremes: Rocks as ultimate refuge for fungi in drylands – Coleine et al. – Mycologia

Bioinformatics

[REVIEW]Emerging computational tools and models for studying gut microbiota composition and function – Park et al. – Current Opinion in Biotechnology

November 27, 2020

Hello from Luebeck!

Today’s digest covers the connection between human diseases and gut microbiome, the gut feeling, secrets about plant growth and vertical stratification in urban spaces. Happy reading and happy black Friday!

General microbiome

Human microbiome and allergy – Montecchiani & Fanos – Pediatric Allergy and Immunology

Early life and childhood

Early Gut Fungal and Bacterial Microbiota and Childhood Growth – Schei et al. – Frontiers in Pediatrics

Oral human microbiome

Characterization of Lactobacilli isolated from carious dentin after selective caries removal and cavity sealing – Damé-Teixeira et al. – Archives of Oral Biology

Human gut microbiome

A Pilot Study: Changes of Intestinal Microbiota of Patients With Non-small Cell Lung Cancer in Response to Osimertinib Therapy – Cong et al. – Frontiers in Microbiology

What connection is there between intestinal microbiota and heart disease? – Poli – European Heart Journal Supplements

The Student-Centered Classroom: The New Gut Feeling – Lyles & Oli – FEMS Microbiology Letters

Animal microbiome

Comparison of the fecal microbiota composition between the blue Sheep (Pseudois nayaur) fed with Lolium perenne and Sorghum sudanense – Wu, Yuan & Pan – Canadian Journal of Microbiology

Plant, root, and soil microbiome

[REVIEW]The plant microbiome: The dark and dirty secrets of plant growth – Tkacz & Poole – Pants People Plant

Water and extremophile microbiome

[PREPRINT]Rapid shift in microbial community structure in a neutral hydrothermal hot spring from Costa Rica – Rojas-Gätjens et al. – bioRxiv

Environment

Vertical Stratification in Urban Green Space Aerobiomes – Robinson et al. – Environmental Health Perspectives

Techniques

Power calculations for detecting differences in efficacy of fecal microbiota donors – Olesen – Contemporary Clinical Trials Communications

November 25, 2020

Human respiratory microbiome

[PREPRINT] Genomic diversity and antimicrobial resistance of Haemophilus colonising the airways of young children with cystic fibrosis – Watts et al. – bioRxiv

Human vaginal microbiome

VALENCIA: a nearest centroid classification method for vaginal microbial communities based on composition – France et al. – Microbiome

Human gut microbiome

Diet influences the functions of the human intestinal microbiome – De Angelis et al. – Scientific Reports

Dietary probiotic and metabolites improve intestinal homeostasis and prevent colorectal cancer – Peng et al. – Food & Function

Animal microbiome

The synergistic tumor growth-inhibitory effect of probiotic Lactobacillus on transgenic mouse model of pancreatic cancer treated with gemcitabine – Chen et al. – Scientific Reports

16S rRNA sequence data of Bombyx mori gut bacteriome after spermidine supplementation – Rajan et al. – BMC Research Notes

Host plant diet affects growth and induces altered gene expression and microbiome composition in the wood white (Leptidea sinapis) butterfly – Näsvall et al. – Molecular Ecology

Effect of sterilization on the canine vaginal microbiota: a pilot study – Rota et al. – BMC Veterinary Research

Bacterial dispersal and drift drive microbiome diversity patterns within a population of feral hindgut fermenters – Stothart et al. – Molecular Ecology

Changes in the faecal bacterial microbiota during hospitalisation of horses with colic and the effect of different causes of colic – Stewart et al. – Equine Veterinary Journal

Microbiome‐Metabolomic Analyses of the Impacts of Dietary Stachyose on Fecal Microbiota and Metabolites in Infants Intestinal Microbiota‐associated Mice – Xi et al. – Science of Food and Agriculture

Bioinformatics

MetaGeneHunt for protein domain annotation in short-read metagenomes – Berlemont et al. – Scientific Reports

SuRF: A new method for sparse variable selection, with application in microbiome data analysis – Liu – et al. – Statistics in Medicine

November 17, 2020

Multi-site human microbiome

Microbiome diversity predicts surgical success in patients with rectovaginal fistula – Leach et al. – International Urogynecology Journal

Human oral microbiome

[REVIEW]Oral Microbiota and Cancer Development – Tuominen & Rautava – Pathobiology

Human vaginal/pregnancy microbiome

Shotgun sequencing of the vaginal microbiome reveals both a species and functional potential signature of preterm birth – Feehily et al. – npj biofilms and microbiomes

Human gut microbiome

[REVIEW]IBDs and the pediatric age: Their peculiarities and the involvement of the microbiota – Cococcioni et al. – Digestive and Liver Disease

Gut microbiome stability and dynamics in healthy donors and patients with non-gastrointestinal cancers – Byrd et al. – JEM

Species-dependent variation of the gut bacterial communities across Trypanosoma cruzi insect vectors – Arias-Giraldo – PLOS One

Gut Microbiota and Cancer Correlates – Malaviya et al. – Probiotic Research in Therapeutics

Short-Chain Fatty Acids and Lipopolysaccharide as Mediators Between Gut Dysbiosis and Amyloid Pathology in Alzheimer’s Disease – Marizzoni et al. – Journal of Alzheimer’s Disease

Built environment (subways, indoor surfaces)
Unravelling the importance of the eukaryotic and bacterial communities and their relationship with Legionella spp. ecology in cooling towers: a complex network – Paranjape et al. – Microbiome

Techniques
Transductomics: sequencing-based detection and analysis of transduced DNA in pure cultures and microbial communities – Kleiner et al. – Microbiome

[REVIEW]NMR: Unique Strengths That Enhance Modern Metabolomics Research – Edison et al. – Analytical Chemistry

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

Study offers “indisputable” link between Alzheimer’s and gut microbiome – Lavars – New Atlas

October 30, 2020

COVID19
Cancer inpatients with COVID-19: A report from the Brazilian National Cancer Institute – de Melo et al. – PLOS One

Few bacterial co-infections but frequent empiric antibiotic use in the early phase of hospitalized patients with COVID-19: results from a multicentre retrospective cohort study in The Netherlands – Karami – et al. – Infectious Diseases

Infection of dogs with SARS-CoV-2 – Sit et al. – Nature

General microbiome/metabolome

Metabolomics of primary cutaneous melanoma and matched adjacent extratumoral microenvironment – Taylor et al. PLOS One

Human gut microbiome

Microbial signature in IgE-mediated food allergies – Goldberg et al. – Genome Medicine

Gut microbiota profiles of treatment-naïve adult acute myeloid leukemia patients with neutropenic fever during intensive chemotherapy – Rattanathammethee et al. – PLOS One

[Book Chapter]Understanding Polyphenols’ Health Effects Through the Gut Microbiota – Selma et al. – Dietary Polyphenols : Their Metabolism and Health Effects

[REVIEW]Gut Microbiota: Its Potential Roles in Pancreatic Cancer – Li et al. – Front. Cell. Infect. Microbiol.

Plant, root, and soil microbiome

Biological invasions alter environmental microbiomes: A meta-analysis – Malacrino et al. – PLOS One

Phages and viruses

[PREPRINT]VirION2: a short- and long-read sequencing and informatics workflow to study the genomic diversity of viruses in nature – Zablocki et al. – bioRxiv

Mycobiome
[REVIEW]T cell immunity to commensal fungi – Scheffold, Bacher & LeibundGut-Landmann – Current Opinion in Microbiology

Bioinformatics

Prometheus, an omics portal for interkingdom comparative genomic analyses – Ko et al. – PLOS One

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

News in Brie! Scientists discover cheese is so smelly because it helps microbes ‘talk’ to the bacteria that makes it ripe – S. Howes – Daily Mail

October 21, 2020

Good morning from Northern Germany,

Today’s selection comprises among others new research about intestinal microbiome and breast cancer (by Koren lab), a perspective about the human microbiome in the 21st century and the diversity in marine sediments. Additionally, we selected a study about linking genetics, microbiome and autoimmunity (multiple sclerosis) in a mouse model and a study about postmortomics.

Conferences

The 3rd Microbiome Movement – Skin Health & Dermatology Summit unites leaders from academia and industry to address the unique challenges that working within the skin microbiome possesses, with the goal to accelerate microbiome-targeted therapeutics and cosmetics.
View the event website for more details.

General microbiome

[Review] Metabolomics Signatures of Aging: Recent Advances – Sunil and Yulan – Aging and Disease

The human microbiome in the 21st century – Rackaityte & Lynch – Nature Communications

Human gut microbiome

The intestinal microbiome, weight, and metabolic changes in women treated by adjuvant chemotherapy for breast and gynecological malignancies – Uzan-Yulzari et al. BMC Medicine

[Review] The Role of the Gut Microbiota in Coronary Heart Disease – Liu et al. – Coronary Heart Disease

[Review] Gut microbial molecules in behavioural and neurodegenerative conditions – Needham, Kaddurah & Mazmanian – Nature Reviews Neuroscience

Animal experiments

Interactions between host genetics and gut microbiota determine susceptibility to CNS autoimmunity – Montgomery et al. – PNAS

Bifidobacterium alters the gut microbiota and modulates the functional metabolism of T regulatory cells in the context of immune checkpoint blockade – Sun et al. – PNAS

Bugs and drugs: a systems biology approach to characterising the effect of moxidectin on the horse’s faecal microbiome – Daniels, Swann & Proudman – Animal Microbiome

A pioneer calf foetus microbiome – Guzman et al. – Scientific Reports

Water and extremophile microbiome

Global diversity of microbial communities in marine sediment – Hoshino et al. – PNAS

Bioinformatics

[Review] Statistical and Machine-Learning Analyses in Nutritional Genomics Studies – Khorraminezhad et al. – nutrients
[Review] A need to consider the evolutionary genetics of host‐symbiont mutualisms – Stoy et al. – Journal of Evolutionary Biology

Techniques

Postmortomics: The Potential of Untargeted Metabolomics to Highlight Markers for Time Since Death – Pesko et al. – OMICS: A Journal of Integrative Biology

October 09, 2020

COVID-19
Face masks: what the data say – Lynne Peeples – Nature

Pregnancy and early life

[REVIEW] Can we prevent allergic disease? Understanding the links between the early life microbiome and allergic diseases of childhood – Petersen & Turvey – Current Opinions in Pediatrics

Human skin microbiome

Atopic Dermatitis and the Role of the Skin Microbiome in Choosing Prevention, Treatment, and Maintenance Options – Baldwin ety al. – Journal of Drugs in Dermatology

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

[PREPRINT] Western-style diet impedes colonization and clearance of gut bacterial pathogens – Gewirtz et al. – bioRxiv

Animal microbiome (for animals in the wild)

Taxonomic profiling of individual nematodes isolated from copse soils using deep amplicon sequencing of four distinct regions of the 18S ribosomal RNA gene – Kenmotsu et al. – PLOS One

The red flour beetle Tribolium castaneum: A model for host-microbiome interactions – Agarwal & Agashe – PLOS One

[PREPRINT] Meta-transcriptomic identification of divergent Amnoonviridae in fish – Turnbull et al. – bioRxiv

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

Metagenome analysis from the sediment of river Ganga and Yamuna: In search of beneficial microbiome – Behera et al. – PLOS One

Phages and viruses

[PREPRINT] Thousands of previously unknown phages discovered in whole-community human gut metagenomes – Benler et al. – bioRxiv

Bioinformatics

Metabolic pathway inference using multi-label classification with rich pathway features – Basher, McLaughlin & Hallam – PLOS Computational Biology

Big Data in metagenomics: Apache Spark vs MPI – Abuin et al. – PLOS One

October 07, 2020

Grant application (US specific grant)
2020 Biocodex Microbiota Foundation US $50,000 grant, supporting cutting edge research on the relationship between gut microbiota and chronic disease.
Deadline: October 15th.
Link: https://www.biocodexmicrobiotafoundation.com/national-call-projects/usa

General microbiome

Understanding the potential of lactobacilli in recurrent UTI prevention – Vagios, Hesham & Mitchel – Microbial Pathogenesis

Throat microbial community structure and functional changes in post-surgery laryngeal carcinoma patients – Hsueh et al. – Applied and Environmental Microbiology

Bacterial diversity and prevalence of antibiotic resistance genes in the oral microbiome – Almeida et al. – PLOS One

Metagenomics of the modern and historical human oral microbiome with phylogenetic studies on Streptococcus mutans and Streptococcus sobrinus – Achtman & Zhou – Philosophical Transactions of the Royal Society B

Pregnancy and early life

In utero human intestine harbors unique metabolomic features including bacterial metabolites – Li et al. – JCI insight

Interactions between Environmental Exposures and the Microbiome: Implications for Fetal Programming – Banerjee, Suter & Aagaard – Current Opinion in Endocrine and Metabolic Research

Human nearly-sterile sites (blood, organs, brain)

Alterations in blood microbiota after colonic cancer surgery – Søby et al. – BJS Open

Human gut microbiome

Estimating molecular preservation of the intestinal microbiome via metagenomic analyses of latrine sediments from two medieval cities – Sabin et al. – Philosophical Transactions of the Royal Society B

Gut microbiota composition in obese and non-obese adult relatives from the highlands of Papua New Guinea – Jonduo et al. – FEMS Microbiology Letters

Fecal Bacteria as Biomarkers for Predicting Food Intake in Healthy Adults – Shinn et al. – The Journal of Nutrition

Animal experiments

Inulin fermentation by lactobacilli and bifidobacteria from dairy calves – Zhu et al. – Applied and Environmental Microbiology

Plant, root, and soil microbiome

Microbial Diversity and Community Structure in Alpine Stream Soil – Rasool et al. – Geomicrobiology Journal

Food microbiology

Impact of dietary fibers in infant formula on gut microbiota and the intestinal immune barrier – Kong et al. – Food & Function

Bioinformatics

[PREPRINT] A framework for comparing microbial networks reveals core associations – Rottjers et al. – bioRxiv

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

Gut health benefits begin in utero – Brita Belli – YaleNews

Medieval poo holds clues to health of modern-day gut microbiome – Sara Rigby – Science Focus

September 25, 2020

Hello from Lübeck/Germany,
today we cover a broad range of microbiome related studies. Of particular interest is a preprint by the Korem lab about use of antibiotics and increase in aggressive behavior in D. melanogaster. This study got already some attention on Twitter and in the press. Furthermore, one preprint covers the C. difficile species problem, investigating the genetic heterogeneity of this species. Last but not least, I would like to mention a paper investigating responses of megakaryocytes, erythroid cells and plasmablasts as hallmarks of severe COVID-19 trajectories.

COVID-19

[PREPRINT] Longitudinal multi-omics analysis identifies responses of megakaryocytes, erythroid cells and plasmablasts as hallmarks of severe COVID-19 trajectories – Bernardes et al. – medRxiv

General microbiome

[PREPRINT] The Clostridioides difficile species problem: global phylogenomic analysis uncovers three ancient, toxigenic, genomospecies – Knight et al. – bioRxiv

Human respiratory microbiome

Longitudinal Changes in Early Nasal Microbiota and the Risk of Childhood Asthma – Toivonen et al. – Pediatrics

Human gut microbiome

[REVIEW] Host–microbiota maladaptation in colorectal cancer – Janney, Pworie & Mann – Nature

Animal experiments

The maternal microbiome modulates fetal neurodevelopment in mice – Vuong et al. – Nature

[PREPRINT] Antibiotics increase aggression behavior and aggression-related pheromones and receptors in Drosophila melanogaster – Grinberg et al. – bioRxiv

Plant, root, and soil microbiome

[PREPRINT] Viruses carrying genes for microbial extremotolerance are abundant and widely dispersed in the Atacama Desert hyperarid soil – Hwang et al. – bioRxiv

Water and extremophile microbiome

[PREPRINT] Enrichment of novel Verrucomicrobia, Bacteroidetes and Krumholzibacteria in an oxygen-limited, methane- and iron-fed bioreactor inoculated with Bothnian Sea sediments – Martins et al. – bioRxiv

Built environment

[PREPRINT] The rise and the fall of a Pseudomonas aeruginosa epidemic lineage in a hospital – Petitjean et al. – bioRxiv

Metabolic traits

Metabolic trait diversity shapes marine biogeography – Deutsch, Penn & Seibel – Nature

Bioinformatics

[Preprint] Inferring microbial co-occurrence networks from amplicon data: a systematic evaluation – Kishore et al. – bioRxiv

Microbes in the news

Tiny bacteria impact our health in big ways – Gina Rich – The Washington Post (KidsPost)

Gut microbiome plays important role in sleep regulation – ScienceDaily