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
Microbiome Digest - Bik's Picks 