Author Archives: Axel Künstner

January 06, 2021

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Good morning, today we selected papers about the cancer microbiome atlas, detection of blood parasites, antibiotics and gut microbiome, metabolome and a new binning approach for metagenomic data using auto-encoders.

General microbiome

The cancer microbiome atlas: a pan-cancer comparative analysis to distinguish tissue-resident microbiota from contaminants – Dohlaman et al. – Cell Host & Microbe

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

Sensitive universal detection of blood parasites by selective pathogen-DNA enrichment and deep amplicon sequencing – Flaherty et al. – Microbiome

Human gut microbiome

Long-Term Impact of Suppressive Antibiotic Therapy on Intestinal Microbiota – Escudero-Sanchez et al. – genes

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

Metagenomics dataset used to characterize microbiome in water and sediments of the lake Solenoe (Novosibirsk region, Russia) – Bryanskaya et al. – Data in Brief

*Metabolome

Changes in the Serum Metabolome of Patients Treated With Broad-Spectrum Antibiotics – Kaskiw et al. – Pathogens and Immunity

Walnut Consumption, Plasma Metabolomics, and Risk of Type 2 Diabetes and Cardiovascular Disease – Guasch-Ferre et al. – The Journal of Nutrition

Bioinformatics

Improved metagenome binning and assembly using deep variational autoencoders – Nissen et al. – Nature Biotechnology

Januar 04, 2021

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Good morning and happy new year! The first post in 2021 is rather short and covers gut microbiota and cancer, FMT, gut microbiota in calves and microbiome/archeaome of two wild animal species.

Human gut microbiome

Dysbiosis of gut microbiota in patients with esophageal cancer – Deng et al. – Microbial Pathogenesis

[REVIEW]Immunotherapy in Solid Tumors and Gut Microbiota: The Correlation—A Special Reference to Colorectal Cancer – Koulouridi et al. – Cancers

Fecal Microbiota Transplantation Is Highly Effective in Real-World Practice: Initial Results From the FMT National Registry – Kelly et al. – Gastroenterology

Fecal microbiota transplantation for graft-versus-host disease in children and adults: methods, clinical effects, safety – Goloshchapov et al. – Therapeutic archive (Article in Russian)

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

Analysis of the developing gut microbiota in young dairy calves—impact of colostrum microbiota and gut disturbances – Hang, Wredle & Dicksved – Tropical Animal Health and Production

Animal microbiome (for animals in the wild)

Consistent patterns in 16S and 18S microbial diversity from the shells of the common and widespread red-eared slider turtle (Trachemys scripta) – Parks, Kedy & Skalla – PLOS One

Archaeal communities of low and high microbial abundance sponges inhabiting the remote western Indian Ocean island of Mayotte – Polonia et al. – Antonie van Leeuwenhoek Journal of Microbiology

December 23, 2020

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Good morning from Northern Germany! It is almost Xmas. Today’s microbiome digest is rather long and comprises some interesting findings about c-section and the gut microbiome in early life, human breast milk, chronic pain, antimicrobial resistance, imbalance of the gut microbiome in relation to Parkinon’s disease and COVID19, diet, honey bees (two pre-prints), roundup, and last but not least some bioinformatic papers. Additionally, we select some interesting reviews. Of specific interest is a study about showing reveals poor correlations in microbial taxonomic abundance between humans and mice after gnotobiotic transfer.

General microbiome

Sequence variant analysis reveals poor correlations in microbial taxonomic abundance between humans and mice after gnotobiotic transfer – Fouladi et al. – The ISME Journal

Application of ecological and evolutionary theory to microbiome community dynamics across systems – McDonald, Marchesi & Koskella – Proceedings of the Royal Society B

[BOOK CHAPTER]Salivary and Urinary Metabolome in Pediatric Obesity and Metabolic Syndrome – Troisi et al. – Obesity and Diabetes

Human early life microbiome

Cesarean delivery is associated with decreased beneficial gut microbes and increased pathobionts and butyrate excretion: a longitudinal study over the first year of life. – Mueller et al – BJOG

Human oral microbiome

[OPINION]Future directions for studying resilience of the oral ecosystem – Zemouri et al. – British Dental Journal

Human milk microbiome

Maternal diet alters human milk oligosaccharide composition with implications for the milk metagenome – Seferovic et al. – Scientific Reports

Mapping the Human Milk Microbiome: Impetus for a Long-Awaited Renaissance in Maternal and Infant Nutrition Research? – McGuire & McGuire – The Journal of Nutrition

[PREVIEW]Breast Milk Modulates Transgenerational Immune Inheritance – Zimmermann & Macpherson – Cell

An Immunologic Mode of Multigenerational Transmission Governs a Gut Treg Setpoint – Ramanan et al. – Cell

Human respiratory/lung microbiome

[REVIEW]The Lung Microbiome and Pneumonia – Pettigrew, Tanner & Harris

[REVIEW]Microbiome: A Supportive or a Leading Actor in Lung Cancer? – Martins, Mendes & Schmitt – Pathobiology

Human skin microbiome

[REVIEW]Skin and Gut Microbiome in Psoriasis: Gaining Insight Into the Pathophysiology of It and Finding Novel Therapeutic Strategies – Chen et al. – Frontiers in Microbiology

Human gut microbiome

An association between chronic widespread pain and the gut microbiome – Freidin et al. – Rheumatology

The Gut Microbiome as a Reservoir for Antimicrobial Resistance – Anthony et al. – The Journal of Infectious Diseases

[REVIEW]Dietary modification of gut microbial metabolism protects the kidney – Carney – Nature Reviews Nephrology

Gut Microbiome Imbalance and Neuroinflammation: Impact of COVID‐19 on Parkinson’s Disease – Follmer – Movement Disorders

US nativity and dietary acculturation impact the gut microbiome in a diverse US population – Peters et al. – The ISME Journal

[REVIEW]Gut Microbiota Status in COVID-19: An Unrecognized Player? – Zeppa et al. – Front. Cell. Infect. Microbiol.

Animal microbiome

[PREPRINT]Honeybee gut microbiota modulates host behaviors and neurological processes – Zhang et al. – bioaRxiv

[PREPRINT]Honeybee genetics shape the strain-level structure of gut microbiota in social transmission – Wu et al. – bioRxiv

Description of the microbiota in epidermal mucus and skin of sharks (Ginglymostoma cirratum and Negaprion brevirostris) and one stingray (Hypanus americanus) – Caballero et al. – PeerJ

Roundup causes embryonic development failure and alters metabolic pathways and gut microbiota functionality in non-target species – Microbiome – Suppa et al. – Microbiome

Plant, root, and soil microbiome

Influence of vintage, geographic location and cultivar on the structure of microbial communities associated with the grapevine rhizosphere in vineyards of San Juan Province, Argentina – Aguilar et al. – PLOS One

[REVIEW]Restoring degraded microbiome function with self-assembled communities – Gutierrez et al. – FEMS Microbiology Ecology

Combining whole-genome shotgun sequencing and rRNA gene amplicon analyses to improve detection of microbe–microbe interaction networks in plant leaves – Regalado et al. – The ISME Journal

Bioinformatics/Data analysis

A joint modeling approach for longitudinal microbiome data improves ability to detect microbiome associations with disease – PLOS Computation Biology – Luna, Mansbach & Shaw

Predicting Nash equilibria for microbial metabolic interactions – Cai, Tan & Chan – Bioinformatics

microeco: An R package for data mining in microbial community ecology – Liu et al. – FEMS Microbiology Ecology

[REVIEW]Multi-omics data integration considerations and study design for biological systems and disease – Graw et al. – Molecular Omics

Techniques

[PREPRINT]Improved microbial community characterization of 16S rRNA via metagenome hybridization capture enrichment – Beaudry et al. – bioRxiv

December 16, 2020

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COVID19

Inferring the effectiveness of government interventions against COVID-19 – Brauner et al. – Science

COVID 19 mortality: Probable role of microbiome to explain disparity – Kumar & Chander – Medical Hyptheses

General microbiome

[PREPRINT] Theory of (antimicrobial) relativity: When competitors determine a species’ drug sensitivity. – Reding – bioRxiv

Human respiratory microbiome

Metagenomic Next-Generation Sequencing of Nasopharyngeal Specimens Collected from Confirmed and Suspect COVID-19 Patients – Mostafa et al. – mBio

Human oral microbiome

Variation in oral microbiome is associated with future risk of lung cancer among never-smokers – Hosgood et al. – Lung cancer

Human gut microbiome

Effect of an 8-week Exercise Training on Gut Microbiota in Physically Inactive Older Women – Zhong et al. – Int J Sports Med

Vitamin D metabolites and the gut microbiome in older men – Thomas et al. – Nature Communications

Animal microbiome

[PREPRINT] Longitudinal profiling of the macaque vaginal microbiome reveals similarities to diverse human vaginal communities: implications for use as a pre-clinical model for bacterial vaginosis – Rhoades et al. – bioRxiv

The earthworm microbiome is resilient to exposure to biocidal metal nanoparticles – Swart et al. – Environmental Pollution

Plant, root, and soil microbiome

Environmental microbiome mapping as a strategy to improve quality and safety in the food industry – Filippis et al. – Current Opinion in Food Science

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

Nitrosophilus alvini gen. nov., sp. nov., a hydrogen-oxidizing chemolithoautotroph isolated from a deep-sea hydrothermal vent in the East Pacific Rise, inferred by a genome-based taxonomy of the phylum “Campylobacterota” – Shiotani et al. – PLOS One

Techniques

A rapid approach to profiling diverse fungal communities using the MinION™ nanopore sequencer – Mafune et al. – BioTechniques

[PREPRINT] Microbe-seq: high-throughput, single-microbe genomics with strain resolution, applied to a human gut microbiome – Zheng et al. – bioRxiv

Microbes in the news

Oral Microbiome Diversity and Species Abundance Linked to Lung Cancer in Nonsmokers

December 08, 2020

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General microbiome

The Microbial Conveyor Belt: Connecting the Globe through Dispersion and Dormancy – Mestre & Höfer – Trends in Microbiology

Microbiomes for All – Muth & Caplan – Frontiers in Microbiology

Human oral microbiome

[REVIEW]The Oral Host–Microbial Interactome: An Ecological Chronometer of Health? – Freire, Nelson & Edlund – Trends in Microbiology

Human vaginal microbiome

Impact of vaginal microbiome communities on HIV antiretroviral-based pre-exposure prophylaxis (PrEP) drug metabolism – Cheu et al. – PLOS Pathogens

Human gut microbiome

The Effect of Probiotics Supplementation on Gut Microbiota After Helicobacter pylori Eradication: A Multicenter Randomized Controlled Trial – Tang et al. – Infectious Diseases and Therapy

Therapeutic potential of natural products against atherosclerosis: Targeting on gut microbiota – Zhao et al. – Pharmacological Research

Glycan utilization systems in the human gut microbiota: a gold mine for structural discoveries – Tamura & Brumer – Current Opinion in Structural Biology

Animal microbiome (for animals in the wild)

Distinct gut microbiotas between southern elephant seals and Weddell seals of Antarctica – Kim, Cho & Lee – Journal of Microbiology

Plant, root, and soil microbiome

Soil texture and properties rather than irrigation water type shape the diversity and composition of soil microbial communities – Obayomi et al. – Applied Soil Ecology

Microbes in space

[BOOK CHAPTER]Antarctic Bacteria as Astrobiological Models – Abbott & Pearce – Extremophiles as Astrobiological Models

Bioinformatics

MANTA, an integrative database and analysis platform that relates microbiome and phenotypic data – Chen et al. – PLOS One

[REVIEW]Measuring the microbiome: best practices for developing and benchmarking microbiomics methods – Bokulich et al. – Computational and Structural Biotechnology Journal

[REVIEW]Seeing the forest for the trees: retrieving plant secondary biochemical pathways from metabolome networks – Desmet et al. – Computational and Structural Biotechnology Journal

Evaluation of Single Sample Network Inference Methods for Metabolomics-Based Systems Medicine – Jahagirdar & Saccenti – Journal of Proteome Research

December 04, 2020

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General microbiome

Highly multiplexed spatial mapping of microbial communities – Shi et al. – Nature

Human respiratory microbiome

Comparison of the human microbiome in adults and children with chronic rhinosinusitis – Park et al. – PLOS One

Human gut microbiome/mycobiome

Gut mycobiomes are altered in people with type 2 Diabetes Mellitus and Diabetic Retinopathy – Jayasudha et al. – PLOS One

Mucosa-Associated Microbiota in Patients with Irritable Bowel Syndrome: A Comparison of Subtypes – Matsumoto et al. – Digestion

[REVIEW]The Role of the Gut Microbiota and the Immune System in the Development of Autism – Lungba et al. – Cureus Journal of Medical Science

Animal microbiome

A shotgun metagenomic investigation of the microbiota of udder cleft dermatitis in comparison to healthy skin in dairy cows – Ekman et al. – PLOS One

Gut microbiota is associated with protection against Marek’s disease virus infection in chickens – Bavananthasivam – Virology

Stingless bees and microbial interactions – de Paula et al. – Current Opinion in Insect Science

Bioinformatics

CoMA – an intuitive and user-friendly pipeline for amplicon-sequencing data analysis – Hupfauf et al. – PLOS One

December 02, 2020

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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

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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

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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

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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