Good morning everyone. Today’s digest includes various interesting articles such as: 1) mNGS-based approach for broad-range detection of pathogens associated with CNS infections, 2) dynamics of diarrheal pathogenesis and antimicrobial resistance transmission using gut microbiome and resistome profiling, 3) comparison urinary and bladder mucosa-associated microbiome composition in bladder cancer patients, 4) regulation of vaginal microbiome composition and stability by ovarian hormones, diet and exercise, 5) Chokeberry polyphenols can reduce the body weight of HFD-fed rats by accelerating energy homeostasis and thermogenesis in interscapular brown adipose tissue, 6) Comparison of taxonomic composition and diversity of bacterial and fungal communities in synanthropic and non-synanthropic mound-building mouse, and 7) an information retrieval system for large metagenomic datasets to recover missing content from genome bins. Enjoy reading. Happy weekend.

General microbiome

Commentary: mSphere of Influence: Translating Gut Microbiome Studies To Benefit Human Health – Anna M. Seekatz – mSphere

A metagenomics-based diagnostic approach for central nervous system infections in hospital acute care setting – Mohammad Rubayet Hasan – Scientific Reports

Human microbiome

Metagenomic analysis of gut microbiome and resistome of diarrheal fecal samples from Kolkata, India, reveals the core and variable microbiota including signatures of microbial dark matter – Rituparna De – Gut Pathogens

Bladder cancer-related microbiota: examining differences in urine and tissue samples– Bassel Mansour – Scientific Reports

Daily Vaginal Microbiota Fluctuations Associated with Natural Hormonal Cycle, Contraceptives, Diet, and Exercise – Stephanie D. Song – mSphere

Dynamics of the lung microbiome in intensive care patients with chronic obstructive pulmonary disease and community-acquired pneumonia – Wei-Chang Huang – Scientific Reports

Animal microbiome / Animal experiments

The polyphenol-rich extract from chokeberry (Aronia melanocarpa L.) modulates gut microbiota and improves lipid metabolism in diet-induced obese rats – Yue Zhu – Nutrition and Metabolism

Changes in the gut microbiota mediate the differential regulatory effects of two glucose oxidases produced by Aspergillus niger and Penicillium amagasakiense on the meat quality and growth performance of broilers – Shengru Wu – Journal of Animal Science and Biotechnology

The effects of atrazine on the microbiome of the eastern oyster: Crassostrea virginica – Adrian Britt – Scientific Reports

How being synanthropic affects the gut bacteriome and mycobiome: comparison of two mouse species with contrasting ecologies – Barbora Bendová – BMC Microbiology

Fruit and vegetable microbiome

Exploring bacteria diversity in commercialized table olive biofilms by metataxonomic and compositional data analysis – Antonio Benítez-Cabello – Scientific Reports

Plant, root and soil microbiome

Deconstructing the Soil Microbiome into Reduced-Complexity Functional Modules – Dan Naylor – mBio

Water microbiome

Metagenomic water quality monitoring with a portable laboratory – Kishor Acharya – Water Research

Methods

Exploring neighborhoods in large metagenome assembly graphs using spacegraphcats reveals hidden sequence diversity – C. Titus Brown – Genome Biology

Good morning! Today there are not many papers, but there are two interesting highlights. The first being a COVID paper analysing the immunological profiles of patients, suggesting an immune-based therapeutic intervention may be the way to go. The second paper analysing the oral microbiome in oral cancer patients, showing significant alterations in diversity and specific genuses in these patients.

Enjoy!

COVID-19

Immunological and inflammatory profiles in mild and severe cases of COVID-19. Song et al. Nature Communications.

Human microbiome

Oral microbial dysbiosis and its performance in predicting oral cancer. Su et al. Carcinogenesis.

Animal microbiome

Potential of indigenous Bacillus spp. as probiotic feed supplements in an extruded low‐fish‐meal diet for juvenile olive flounder, Paralichthys olivaceus. Niu et al. Journal of the World Aquaculture Society.

Animal experiments

Glyphosate-based herbicides influence antioxidants, reproductive hormones and gut microbiome but not reproduction: A long-term experiment in an avian model. Ruuskanen et al. Environmental pollution.

Evidence of Microbiome-Drug Interactions Between the Antimalarial Lumefantrine and Gut Microbiota in Mice. Ippolito et al. The American Journal of Tropical Medicine and Hygiene.

Plant, root and soil microbiome

The bacterial community and metabolome dynamics and their interactions modulate fermentation process of whole crop corn silage prepared with or without inoculants. Xu et al. Society for Applied Microbiology.

Water and extremophile microbiome

Host and environmental determinants of microbial community structure in the marine phyllosphere. Vogel et al. PLOS ONE.

God morgon!

Good morning from Sweden. Another new week and another new digest! Today’s digest is very light with only a few articles. There is an interesting preprint which reports that the SARS-CoV-2 spike protein variant D614G leads to increased infectivity and the virus might have acquired this mutation during human-to-human transmission as this mutation is not seen in the original virus that infects the non-human hosts. This might be the reason why about 97% of the nCoV19 isolates have this mutation. However, the good news is that the neutralizing antibodies against the wildtype virus still retain the ability to target this mutant virus. Another interesting commentary published in Microbiome journal revisits important concepts in microbiome biology and is a must-read for all the microbiome enthusiasts. Elsewhere in the digest is a study on microbial succession in deep-sea hydrothermal vents, microbial communities of small brown planthopper (Laodelphax striatellus) and Shrimp (Litopenaeus vannamei), and thermophilic digestion of biowaste.

Happy reading and have a great week!

COVID 19

Preprint: SARS-CoV-2 Spike protein variant D614G increases infectivity and retains sensitivity to antibodies that target the receptor binding domain – Leonid Yurkovetskiy, et al.

General Microbiome

Fine-scale succession patterns and assembly mechanisms of bacterial community of Litopenaeus vannamei larvae across the developmental cycle – Yanting Wang, et al. – Microbiome

Syntrophic acetate oxidation replaces acetoclastic methanogenesis during thermophilic digestion of biowaste – Stefan Dyksma, et al. – Microbiome

Recent infection by Wolbachia alters microbial communities in wild Laodelphax striatellus populations – Xing-Zhi Duan, et al. – Microbiome

Microbiome definition re-visited: old concepts and new challenges – Gabriele Berg, et al. – Microbiome

Microbial succession during the transition from active to inactive stages of deep-sea hydrothermal vent sulfide chimneys – Jialin Hou, et al. – Microbiome

Pregnancy and early life
Natural environments in the urban context and gut microbiota in infants – Neilsen et al. – Environment International

Human nearly-sterile sites
Breast cancer colonization by Fusobacterium nucleatum accelerates tumor growth and metastatic progression – Parhi et al. – Nature Communications

Enrichment of the airway microbiome in people living with HIV with potential pathogenic bacteria despite antiretroviral therapy – Rofael et al. – EClinicalMedicine

Human microbiome in vitro and ex vivo experiments
Triclosan has a robust, yet reversible impact on human gut microbial composition in vitro – Mahalak et al. – PLOS One

Animal experiments
Alterations of gut microbiota and serum bile acids are associated with parenteral nutrition-associated liver disease – Wang et al. – Journal of Pediatric Surgery

Colonic microbiome profiles for improved feed efficiency can be identified despite major effects of farm of origin and contemporary group in pigs – Vigors et al. – Animal

Gut microbiota profiles of commercial laying hens infected with tumorigenic viruses – Wan et al. – BMC Veterinary Research

Alterations of gut microbiota contribute to the progression of unruptured intracranial aneurysms – Li et al. – Nature Communications

Animal microbiome
Review: The Effects of Nutrition on the Gastrointestinal Microbiome of Cats and Dogs: Impact on Health and Disease – Wernimont et al. – Frontiers in Microbiology

Individual and Site-Specific Variation in a Biogeographical Profile of the Coyote Gastrointestinal Microbiota – Sugden et al. – Microbial Ecology

Assessment of bacterial diversity of Rhipicephalus microplus ticks from two livestock agroecosystems in Antioquia, Colombia – Segura et al. – PLOS One

Microbiome diversity in Diaphorina citri populations from Kenya and Tanzania shows links to China – Ajene et al. – PLOS One

Plant, root, and soil microbiome
Metagenomics analysis of fungal communities associated with postharvest diseases in pear fruits under the effect of management practices – Zambounis et al. – Archives of Microbiology

Water and extremophile microbiome
The Efficacy of Hydrogen Peroxide in Mitigating Cyanobacterial Blooms and Altering Microbial Communities across Four Lakes in NY, USA – Lusty and Gobler – Toxins

Seasonal effects of river flow on microbial community coalescence and diversity in a riverine network – Luo et al. – FEMS Microbiology Ecology

Microbial community composition across a coastal hydrological system affected by submarine groundwater discharge (SGD) – Adyasari et al. – PLOS One

The contribution of microbial communities in polymetallic nodulesto the diversity of the deep-sea microbiome of the Peru Basin(4130–4198 m depth) – Molari et al. – Biogeosciences

Probiotics / prebiotics
Review: Toward a systematic design of smart probiotics – Choudhary and Mahadevan – Current Opinion in Biotechnology

A Novel Non-Digestible, Carrot-Derived Polysaccharide (cRG-I) Selectively Modulates the Human Gut Microbiota while Promoting Gut Barrier Integrity: An Integrated In Vitro Approach – Van den Abbeele et al. – Nutrients

Bioinformatics
Review: What Is Metagenomics Teaching Us, and What Is Missed? – New and Brito – Annual Review of Microbiology

Human microbiome

Analysis of the diversity of intestinal microbiome and its potential value as a biomarker in patients with schizophrenia: A cohort study. – Pan et al. – Psychiatry Research

A longitudinal study of the development of the saliva microbiome in infants 2 days to 5 years compared to the microbiome in adolescents. – Holferson et al. – Scientific Reports

Gut microbiome

Longitudinal analysis reveals transition barriers between dominant ecological states in the gut microbiome. – Levy et al. – PNAS

Genome-wide associations of human gut microbiome variation and implications for causal inference analyses. – Hughes et al. – Nature Microbiology

Cancer and the microbiome. – Ashray Gunjur. The Lancet

Food microbiology

Influences of Ingredients and Bakers on the Bacteria and Fungi in Sourdough Starters and Bread – Reese et al. – mSphere

Plant, root and soil microbiome

Effects of zinc pollution and compost amendment on the root microbiome of a metal tolerant poplar clone. – Guarino et al. – Frontier in Microbioloy

New insights into the distributions of nitrogen fixation and diazotrophs revealed by high-resolution sensing and sampling methods. – Tang et al. – The ISME Journal

Language of plant-microbe-microbe interactions in rhizospheric ecosystems. – Khare et al. – Molecular Aspects of Plant Benefitial Microbes in Agriculture

Environmental microbiology

Editorial: Microbial Ecology in Reservoirs and Lakes. Zhang et al. – Frontier in Microbiology

Natural Holobiome Engineering by Using Native Extreme Microbiome to Counteract the Climate Change Effects. – Rodriguez and Duran – Frontiers in Bioengineering and Biotechnology.