October 13, 2020

Today’s mid-week digest is about – meta analysis of metabolic benefits of probiotics, probiotics and synbiotics, microbiome association with narcolepsy type 1, design of microbial consortium for reduced C. difficle colonization, new sequencing technique for pathogen identification in cerebrospinal fluid and many more… Happy reading!

Human microbiome

The effect of probiotics, prebiotics or synbiotics on metabolic outcomes in individuals with diabetes: a systematic review and meta-analysis – Patricia M. Bock – Diabetologia

Effect of a Nonoptimal Cervicovaginal Microbiota and Psychosocial Stress on Recurrent Spontaneous Preterm Birth – Kristin D. Gerson – American Journal of Perinatology

Targeting the microbiome-gut-brain axis for improving cognition in schizophrenia and major mood disorders: A narrative review – Miquel Bioque – Progress in Neuro-Psychopharmacology and Biological Psychiatry

Inflammatory Bowel Disease Environmental Risk Factors: Diet and Gut Microbiota – Sarah Altajar – Current Gastroenterology Reports

Co‐ and polymicrobial infections in the gut mucosa: the host‐microbiota‐pathogen perspective – Teresa Frisan – Cellular Microbiology

Gut microbiota composition is associated with narcolepsy type 1 – Alexandre Lecomte – Neurology

A parental transcriptional response to microsporidia infection induces inherited immunity in offspring – Alexandra R. Willis – BioRxiv

Melamine contamination and associated health risks: Gut microbiota does make a difference – Meenakshi Rajpoot – Biotechnology and Applied Biochemistry

Animal microbiome

Rational design of a microbial consortium of mucosal sugar utilizers reduces Clostridiodes difficile colonization – Fátima C. Pereira – Nature Communications

Effects of seasonality and previous logging on faecal helminth-microbiota associations in wild lemurs – I. I. de Winter – Scientific Reports

Bacterial community analysis on the different mucosal immune inductive sites of gastrointestinal tract in Bactrian camels – Wang-Dong Zhang – PlosOne

Sows affect their piglets’ faecal microbiota until fattening but not their Salmonella enterica shedding status – Guillaume Larivière‐Gauthier – Letters in Applied Microbiology

Plant, root and soil microbiome

Comparison of soil microbial community between reseeding grassland and natural grassland in Songnen Meadow – Ruifen Zhu – Scientific Reports

Evidence for signatures of ancient microbial life in paleosols – Katharina Frindte – Scientific Reports

Techniques

Pathogen identification in culture-negative cerebrospinal fluid specimens of patients with purulent meningitis using next-generation sequencing technology – Xin Men – International Journal of Clinical Experimental Pathology

October 8, 2020

Greetings!!
Congratulations to the Nobel prize winners in Chemistry : Emmanuelle Charpentier and Jennifer A. Doudna for the discovery of “Genetic scissors: a tool for rewriting the code of life- the CRISPR/Cas9 genetic scissors.” Today’s brief digest covers a wide range of articles on early life microbiome to respiratory microbiome. Happy reading!!!

General microbiome
Electrochemical Investigation of Thiobacillus denitrificans in a Bacterial Composite – Abada et al – Journal of the Electrochemical Society

Pregnancy and early life
Review: Can we prevent allergic disease? Understanding the links between the early life microbiome and allergic diseases of childhood – Petersen and Turvey – Current Opinion in Pediatrics

Multi-site human microbiome
Nutritional Targeting of the Microbiome as Potential Therapy for Malnutrition and Chronic Inflammation – Schröder et al – Nutrients

Human respiratory microbiome
Airway bacterial and fungal microbiome in chronic obstructive pulmonary disease – Liu et al – bioRxiv

Human gut microbiome
Review: Mechanistic insight into the gut microbiome and its interaction with host immunity and inflammation – Xue et al – Animal Nutrition

Ethanol extract of Centella asiatica alleviated dextran sulfate sodium-induced colitis via restoration on mucosa barrier and gut microbiota homeostasis – Li et al – Journal of Ethnopharmacology

Development of a three-compartment in vitro simulator of the Atlantic Salmon GI tract and associated microbial communities: SalmoSim – Kazlauskaite et al – bioRxiv

Time-dependent modulation of gut microbiome in response to systemic antifungal agents – Udawatte et al – bioRxiv

Animal microbiome
North American fireflies host low bacterial diversity – Green et al – bioRxiv

Plant, root, and soil microbiome
Anthropogenic Invasion of Micromycetes to Undisturbed Ecosystems of the Larsemann Hills Oasis (East Antarctica) – Vlasov et al – Russian Journal of Biological Invasions

Larch or Mongolian pine? Effects of tree species on soil properties and microbial biomass with the consideration of afforestation time – Teng et al – Ecological Engineering

Water and extremophile microbiome
Understanding the microbial trends in a nitritation reactor fed with primary settled municipal wastewater – Pedrouso et al – Separation and Purification Technology

Microbiome community and complexity indicate environmental gradient acclimatisation and potential microbial interaction of endemic coral holobionts in the South China Sea – Chen et al – Science of The Total Environment

Microbial community structure in the river sediments from upstream of Guanting Reservoir: potential impacts of reclaimed water recharge – Xie et al – Science of The Total Environment

Food microbiology
Next-generation sequencing to enhance the taxonomic resolution of the microbiological analysis of meat and meat-derived products – Reckem et al – Current Opinion in Food Science

Techniques
CRISPR/Cas12a mediated genome engineering in photosynthetic bacteria – Zhang et al – bioRxiv

October 2, 2020

Today’s exciting updates – FMT method to restore normal microbial development in caesarean-born infants, mechanism unveiled how dietary tryptophan improves alcohol induced liver injury, advance in droplet based microfluidics to study host-microbiome interactions, prebiotics encapsulation of probiotic to suppress colon cancer and new hope to curb plastic waste by discovery of plastic-eating enzyme cocktail. Happy weekend, stay safe!

General microbiome

Eligible blood donors’ decisions about donating stool for fecal microbiota transplantation: Does ambivalence play a role? – Melissa K. Hyde – Transfusion

Microbiota-Dependent Effects of IL-22 – Morsal Sabihi – Cells

Human microbiome

Maternal Fecal Microbiota Transplantation in Cesarean-Born Infants Rapidly Restores Normal Gut Microbial Development: A Proof-of-Concept Study – Katri Korpela – Cell

Comparative analysis of the tonsillar microbiota in IgA nephropathy and other glomerular diseases – Ji In Park – Scientific Reports

Dysbiosis in the oral microbiomes of anti-CCP positive individuals at risk of developing rheumatoid arthritis – Zijian Cheng – Annals of the Rheumatic Diseases

Animal microbiome

Microbiota tryptophan metabolism induces aryl hydrocarbon receptor activation and improves alcohol-induced liver injury – Laura Wrzosek – Gut

Faecal microbiota transplant from aged donor mice affects spatial learning and memory via modulating hippocampal synaptic plasticity- and neurotransmission-related proteins in young recipients – Alfonsina D’Amato – Microbiome

Competitive reduction of poultry-borne enteric bacterial pathogens in chicken gut with bioactive Lactobacillus casei – Zajeba Tabashsum – Scientific Reports

Offspring susceptibility to metabolic alterations due to maternal high-fat diet and the impact of inhaled ozone used as a stressor – Samantha J. Snow – Scientific Reports

Beneficial effects of mung bean seed coat on the prevention of high-fat diet-induced obesity and the modulation of gut microbiota in mice – Dianzhi Hou – European Journal of Nutrition

Prebiotics‐Encapsulated Probiotic Spores Regulate Gut Microbiota and Suppress Colon Cancer – Di‐Wei Zheng – Advanced Materials

Multi-Omic Analysis Reveals Different Effects of Sulforaphane on the Microbiome and Metabolome in Old Compared to Young Mice – Se-Ran Jun – Microorganisms

Plant microbiome

Protists as catalyzers of microbial litter breakdown and carbon cycling at different temperature regimes – Stefan Geisen – Isme Journal

Techniques

Investigating host-microbiome interactions by droplet based microfluidics – Alexandra S. Tauzin – Microbiome

Non-specific amplification of human DNA is a major challenge for 16S rRNA gene sequence analysis – Sidney P. Walker – Scientific Reports

Non-microbiology picks

Plastic-eating enzyme ‘cocktail’ heralds new hope for plastic waste – Science Daily

September 2, 2020

Greetings for the month of September: the Haervest-monath (Harvest Month). Today’s microbiome digest consists of a cool editorial article on hidden theatre of microbes. The digest also features two interesting reviews; first one detailing the role of skin microbiota in forensic sciences and the second one with focus on association of sponges and their microbiome.

Let’s celebrate the month of September with some fascinating microbiome studies.

There are flowers enough in the summertime,
More flowers than I can remember—
But none with the purple, gold, and red
That dye the flowers of September!

—Mary Howitt (1799-1888)

General microbiome
*Editorial: Unveiling the Hidden Theatre of Microbes – Böttcher T – ChemBioChem

Chitosan-chelated zinc modulates cecal microbiota and attenuates inflammatory response in weaned rats challenged with Escherichia coli – Feng et al – Journal of Microbiology

Multi-site human microbiome
Potential Associations Among Alteration of Salivary miRNAs, Saliva Microbiome Structure, and Cognitive Impairments in Autistic Children – Ragusa et al – Int. J. Mol. Sci.

Human respiratory microbiome
Review: The importance of airway and lung microbiome in the critically ill – Martin-Loeches et al – Critical Care

Human skin microbiome
A Novel Mycovirus Evokes Transcriptional Rewiring in the Fungus Malassezia and Stimulates Beta Interferon Production in Macrophages – Clancey et al – mBio

A Novel Virus Alters Gene Expression and Vacuolar Morphology in Malassezia Cells and Induces a TLR3-Mediated Inflammatory Immune Response – Park et al – mBio

*Review: Challenges in Human Skin Microbial Profiling for Forensic Science: A Review – Neckovic et al – Genes

Human gut microbiome
Context-aware dimensionality reduction deconvolutes gut microbial community dynamics – Martino et al – Nat Biotechnol

Animal microbiome
*The relationship between microbiomes and selective regimes in the sponge genus Ircinia – Kelly et al – bioRxiv

Techniques
Flow cytometry with cell sorting and sequencing as a tool for the study of the Humboldt Current krill stomach microbiota – Henriquez-Castillo et al – bioRxiv

Microbes in the news
EurekAlert News: Researchers receive $3 million NSF grant to ‘understand the rules of life – Zhou J

September 1, 2020

Today’s post consists of review article on short chain fatty acids, research articles on efficacy of fecal microbiota transplant in patients with C. difficle infection and comorbities, identification of potential microbial biomarkers for preterm birth and a new technique to perform ultrafast microbial community analysis. Happy reading!

General microbiome

A systematic review of the effect of dietary pulses on microbial populations inhabiting the human gut – C.P.F. Marinangeli – Beneficial Microbes

Short chain fatty acids in human gut and metabolic health – E E Blaak – Beneficial Microbes

Human microbiome

The gut microbiome–derived metabolite trimethylamine N-oxide modulates neuroinflammation and cognitive function with aging – Vienna E. Brunt – Geroscience

Impact of investigational microbiota therapeutic RBX2660 on the gut microbiome and resistome revealed by a placebo-controlled clinical trial – Suryang Kwak – Microbiome

Fecal Microbiota Transplantation for Recurrent Clostridium difficile Infection in Patients With Multiple Comorbidities: Long-Term Safety and Efficacy Results From a Tertiary Care Community Hospital – Charumathi Raghu Subramanian – Gastroenterology Research

Gut commensal microbiota and decreased risk for Enterobacteriaceae bacteriuria and urinary tract infection – Matthew Magruder – Gut Microbes

Leveraging sequence‐based faecal microbial community survey data to identify alterations in gut microbiota among patients with Parkinson’s disease – Tianyi Ji – European Journal of Neuroscience

Plasma enterobacterial ClpB levels and ClpB- and α-MSH–reactive immunoglobulins in lung cancer patients with and without anorexia – Alessio Molfino – Nutrition

Identification of Potential Biomarkers in the Cervicovaginal Fluid by Metabolic Profiling for Preterm Birth – AbuZar Ansari – Metabolites

Plant microbiome

Suppression of rice planthopper populations without affecting the rice microbiota by the entomopathogenic fungus Metarhizium anisopliae – Yifan Peng – Applied and Environmental Microbiology

Cold Plasma Treatment of Sunflower Seeds Modulates Plant-Associated Microbiome and Stimulates Root and Lateral Organ Growth – Inga Tamošiūnė – Frontiers in Plant Science

Water microbiome

Bradymonabacteria, a novel bacterial predator group with versatile survival strategies in saline environments – Da-Shuai Mu – Microbiome

Techniques

Ultrafast and accurate 16S rRNA microbial community analysis using Kraken 2 – Jennifer Lu – Microbiome

Non-microbiology picks

Clinical characteristics of children and young people hospitalised with covid-19 in the United Kingdom: prospective multicentre observational cohort study – Olivia V Swann – BMJ

August 13, 2020

Today’s updates – microbiome connections in various disease cohorts such as gastric cancer, IBD, anorexia nervosa, obesity and diabetes; information on gut bacterial polyphosphates and o-glycanases and their role in host immunity and mucin breakdown; and new sequencing strategies to identify antibiotic-resistant genes. Happy reading!

General microbiome

Gut microbiota and COVID-19: A superfluous diagnostic biomarker or therapeutic target? – Emily Klann – Clinical Infectious Diseases

Engineered Live Biotherapeutics: Progress and Challenges – Yang Tan – Biotechnology Journal

Human microbiome

Gut microbial co-abundance networks show specificity in inflammatory bowel disease and obesity – Lianmin Chen – Nature Communications

Multi-omics data integration in anorexia nervosa patients before and after weight regain: A microbiome-metabolomics investigation – Alessio Maria Monteleone – Clinical Nutrition

Gastric Microbiome Diversities in Gastric Cancer Patients from Europe and Asia Mimic the Human Population Structure and Are Partly Driven by Microbiome Quantitative Trait Loci – Bruno Cavadas – Microorganisms

Faecal microbiota signatures of IBD and their relation to diagnosis, disease phenotype, inflammation, treatment escalation and anti-TNF response in a European Multicentre Study (IBD-Character) – S. Vatn – Scandinavian Journal of Gastroenterology

A randomized crossover trial on the effect of plant-based compared with animal-based meat on trimethylamine-N-oxide and cardiovascular disease risk factors in generally healthy adults: Study With Appetizing Plantfood—Meat Eating Alternative Trial (SWAP-MEAT) – Anthony Crimarco – Americal Journal of Clinical Nutrition

Whole-blood transcriptome profiling reveals signatures of metformin and its therapeutic response – Monta Ustinova – PlosOne

Microbial Profile During Pericoronitis and Microbiota Shift After Treatment – Xiuling Huang – Frontiers in Microbiology

Animal experiments

Unraveling the camel rumen microbiome through metaculturomics approach for agriculture waste hydrolytic potential – Shweta Srivastava – Archives of Microbiology

Bacterial polyphosphates interfere with the innate host defense to infection – Julian Roewe – Nature Communications

Prominent members of the human gut microbiota express endo-acting O-glycanases to initiate mucin breakdown – Lucy I. Crouch – Nature Communications

Nostoc sphaeroids Kütz polysaccharide and powder enrich a core bacterial community on C57BL/6j mice – Meixia Li – International Journal of Biological Macromolecules

Maternal dietary omega-3 deficiency worsens the deleterious effects of prenatal inflammation on the gut-brain axis in the offspring across lifetime – Q. Leyrolle – Neuropsychopharmacology

Water microbiome

Influence of the polar light cycle on seasonal dynamics of an Antarctic lake microbial community – Pratibha Panwar – Microbiome

Techniques

Light into the darkness: Unifying the known and unknown coding sequence space in microbiome analyses – Chiara Vanni – BioRxiv

Metagenomic next-generation sequencing of rectal swabs for the surveillance of antimicrobial-resistant organisms on the Illumina Miseq and Oxford MinION platforms – Rebecca Yee – European Journal of Clinical Microbiology & Infectious Diseases

July 23, 2020

In today’s digest – duodenal microbiota linked to stunting in children, differential effects of germfree and antibiotic treated mouse models on social behavior, microbial metabolite receptor GPBAR and its interaction with bile acids, review article on engineering microbes to treat diseases and many more…happy reading!

General microbiome

The Microbiota-Gut-Immune-Glia (MGIG) Axis in Major Depression – Leszek Rudzki – Molecular Neurobiology

Engineering the gut microbiota to treat chronic diseases – Noura S. Dosoky – Applied Microbiology and Biotechnology

Human microbiome

Acute and chronic improvement in postprandial glucose metabolism by a diet resembling the traditional Mediterranean dietary pattern: Can SCFAs play a role? – Marilena Vitale – Clinical Nutrition

Linking the duodenal microbiota to stunting in a cohort of undernourished Bangladeshi children with enteropathy – Robert Y. Chen – New England Journal of Medicine

Enterobacterales Infection after Intestinal Dominance in Hospitalized Patients – Krishna Rao – mSphere

Differences in the gut Firmicutes to Bacteroidetes ratio across age groups in healthy Ukrainian population – Alexander Vaiserman – BMC Microbiology

Preprint- Association of gut microbiota with cerebral cortex and cerebrovascular abnormality in human mild traumatic brain injury – Lijun Bai – BioRxiv

Real-world study in infants fed an infant formula with two human milk oligosaccharides – Enriqueta Román – Nutricion Hospitalaria

Animal experiments

Gut microbiome composition differences among breeds impact feed efficiency in swine – Matteo Bergamaschi – Microbiome

Opposing effects of antibiotics and germ-free status on neuropeptide systems involved in social behaviour and pain regulation – Katerina V. A. Johnson – BMC Neuroscience

Local Necrotic Cells Trigger Systemic Immune Activation via Gut Microbiome Dysbiosis in Drosophila – Hina Kosakamoto – Cell Reports

Peanut skin extract ameliorates the symptoms of type 2 diabetes mellitus in mice by alleviating inflammation and maintaining gut microbiota homeostasis – Lan Xiang – Aging

Preprint- Community composition and development of the post-weaning piglet gut microbiome – D. Gaio – BioRxiv

Gut microbiota regulate tumor metastasis via circRNA/miRNA networks – Zhuxian Zhua – Gut Microbes

Porcine circovirus type 2 (PCV2) and Campylobacter infection induce diarrhea in piglets: Microbial dysbiosis and intestinal disorder – Gang Yang – Animal Nutrition

Plant, root and soil microbiome

Populations of the Parasitic Plant Phelipanche ramosa Influence Their Seed Microbiota – Sarah Huet – Frontiers in Plant Science

Domestication-driven changes in plant traits associated with changes in the assembly of the rhizosphere microbiota in tetraploid wheat – Aymé Spor – Scientific Reports

Water microbiome

Preprint- Time series metagenomic sampling of the Thermopyles, Greece, geothermal springs reveals stable microbial communities dominated by novel sulfur-oxidizing chemoautotrophs – A. Meziti – BioRxiv

Preprint- Evaluation of the microbial community structure of potable water samples from occupied and unoccupied buildings using16S rRNA amplicon sequencing – Kimothy L. Smith – BioRxiv

Phages and Viruses

Preprint- Targeting of Mammalian Glycans Enhances Phage Predation in the Gastrointestinal Tract – Sabrina I. Green – BioRxiv

Techniques
Structural basis of GPBAR activation and bile acid recognition – Fan Yang – Nature

Microbes in News

Machine learning analysis reveals less diverse microbiome in children with type 1 diabetes – Healio

July 10, 2020

Today’s digest contains many exciting articles – gut microbiome in precision medicine for cancer, important review on patent protection in microbiome therapeutics, role of the gut microbiota in sympathetic neurons, interaction of pacemaker neurons with the gut microbiota, gut dysbiosis in lupus and many more….Enjoy reading and happy weekend!

General microbiome

Gut microbiome, big data and machine learning to promote precision medicine for cancer – Giovanni Cammarota – Nature Reviews Gastroenterology and Hepatology

Co-evolution and Co-speciation of Host-Gut Bacteria Systems – Mathieu Groussin – Cell Host and Microbe

Microbiome therapeutics and patent protection – Mark J. FitzGerald – Nature Biotechnology

Human microbiome

Fecal Microbiota Transplantation is Safe and Effective in Patients with Clostridioides difficile Infection and Cirrhosis – Yao-WenCheng – CLinial Gastroenterology and Hepatology

Association of Gut Microbiota-Dependent Metabolite Trimethylamine N-Oxide with First Ischemic Stroke – Taoping Sun – Journal of Atherosclerosis and Thrombosis

Dietary Strategies for Maintenance of Clinical Remission in Inflammatory Bowel Diseases: Are We There Yet? – Konstantinos Gkikas – Nutrients

The duodenal microbiome is altered in small intestinal bacterial overgrowth – Gabriela Leite – PlosOne

Faecal microbiota transplantation: A life-saving therapy challenged by commercial claims for exclusivity – Christian LodbergHvas – EClinical Medicine

Animal experiments

Microbiota modulate sympathetic neurons via a gut–brain circuit – Paul A. Muller – Nature

Prototypical pacemaker neurons interact with the resident microbiota – Alexander Klimovich – PNAS

Gut microbiota dysbiosis and altered tryptophan catabolism contribute to autoimmunity in lupus-susceptible mice – Seung-Chul Choi – Science Translational Medicine

The relationship between gut microbiota and short chain fatty acids in the renal calcium oxalate stones disease – Yu Liu – Faseb Journal

Sodium Butyrate Alleviates Mouse Colitis by Regulating Gut Microbiota Dysbiosis – Xiujing Dou – Animals

Dietary sphinganine is selectively assimilated by members of the mammalian gut microbiome – Min-Ting Lee – Journal of Lipid Research

Commentary: Modulating microbiome metabolites in vivo – Chun-Jun Guo – Science

Plant, root and soil microbiome

Quantitative comparison between the rhizosphere effect of Arabidopsis thaliana and co-occurring plant species with a longer life history – Martinus Schneijderberg – ISME Journal

Water microbiome

Anthropogenic dissolved organic carbon and marine microbiomes – Maria Vila-Costa – ISME Journal

Functional foods

Effect of a functional fibre supplement on glycemic control when added to a year-long medically supervised weight management program in adults with type 2 diabetes – Raylene A. Reimer – European Journal of Clinical Nutrition

Prenatal exposure to the probiotic Lactococcus lactis decreases anxiety-like behavior and modulates cortical cytoarchitecture in a sex specific manner – Natalia Surzenko – PlosOne

Non microbiology picks

SARS-CoV-2 is transmitted via contact and via the air between ferrets – Mathilde Richard – Nature Communications

June 3, 2020

Today’s post covers articles on role of microbiome in sepsis, early life microbiota related to cystic fibrosis and respiratory syncitial virus disease, promise and challenge with cancer microbiome, effect of probiotics on intestinal homeostasis after chemotherapy and many more!

General microbiome

Predictive biology: modelling, understanding and harnessing microbial complexity – Allison J. Lopatkin – Nature Reviews Microbiology

The Gut Microbiome’s Role in the Development, Maintenance, and Outcomes of Sepsis – Max W Adelman – Critical Care

The Promise and Challenge of Cancer Microbiome Research – Sumeed Syed Manzoor – Genome Biology

Antidiabetic Effects of Flavan-3-ols and Their Microbial Metabolites – Estefanía Márquez Campos – Nutrients

Human microbiome

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

Strain-resolved microbiome sequencing reveals mobile elements that drive bacterial competition on a clinical timescale – Soumaya Zlitni – Genome Medicine

Comparative Assessment of Faecal Microbial Composition and Metabonome of Swine, Farmers and Human Control – Shiang Chiet Tan – Scientific Reports

Matching Between Donors and Ulcerative Colitis Patients Is Important for Long-Term Maintenance After Fecal Microbiota Transplantation – Koki Okahara – Journal of Clinical Medicine

Preganancy and early life

Alterations in Vaginal Microbiota and Associated Metabolome in Women With Recurrent Implantation Failure – Min Fu – mBio

Development of the Gut Microbiota in Early Life: The Impact of Cystic Fibrosis and Antibiotic Treatment – Maartje Kristensen – Journal of Cystic Fibrosis

Altered Gut Microbiota in Infants Is Associated With Respiratory Syncytial Virus Disease Severity – Jeffrey N Harding – BMC Microbiology

Ecological Succession in the Vaginal Microbiota During Pregnancy and Birth – M A Rasmussen – Isme Journal

Animal experiments

Host genotype and exercise exhibit species-level selection for members of the gut bacterial communities in the mouse digestive system – R. A. Dowden – Scientific Reports

Repetitive, Mild Traumatic Brain Injury Results in a Progressive White Matter Pathology, Cognitive Deterioration, and a Transient Gut Microbiota Dysbiosis – Mariana Angoa-Pérez – Scientific Reports

Association of Gut Microbiota Composition and Function With an Aged Rat Model of Senile Osteoporosis Using 16S rRNA and Metagenomic Sequencing Analysis – Sicong Ma – Aging

Increasing the Hindgut Carbohydrate/Protein Ratio by Cecal Infusion of Corn Starch or Casein Hydrolysate Drives Gut Microbiota-Related Bile Acid Metabolism To Stimulate Colonic Barrier Function – Yu Pi – mSystems

Plant, root and soil microbiome

Using Soil Bacterial Communities to Predict Physico-Chemical Variables and Soil Quality – Syrie M Hermans – Microbiome

Analysis of bacterial and archaeal communities associated with Fogo volcanic soils of different ages – Corinne Biderre-Petit – Fems Microbial Ecology

Water microbiome

Functional potential and assembly of microbes from sediments in a lake bay and adjoining river ecosystem for polycyclic aromatic hydrocarbon biodegradation – Zaisheng Yan – Environmental Microbiology

Functional foods

Effect of Probiotics on the Maintenance of Intestinal Homeostasis After Chemotherapy: Systematic Review and Meta-Analysis of Pre-Clinical Studies – W G Lima – Beneficial Microbes

Non microbiology picks

Racial Disparities in Knowledge, Attitudes and Practices Related to COVID-19 in the USA– Wilson M Alobuia – Journal of Public Health

Ozone Treatment for Elimination of Bacteria and SARS-CoV-2 for Medical Environments – Craig Westover – BioRxiv

Clearing up of toxic pollutants using a bacterial protein

A science communication commentary on a recently published paper


Most pollutants are introduced in our environment in the form of herbicides, pesticides, and industrial effluents. The aromatic phenolic compounds, produced by a variety of industries, including phenol-formaldehyde resin, petrochemical plants, coal conversion, and leather processing make up for a major percentage of these pollutants. Improper treatment of these toxic pollutants can lead to heavily contaminated soil and groundwater.

Microorganisms particularly the bacterial species termed as Pseudomonas sp. have been used for a long time to clean up phenol from water in treatment plants. One such (methyl) phenol-degrading strain Pseudomonas putida KCTC 1452 has been studied with respect to its metabolic pathways involved in biodegradation.  The bacterium uses a protein called as DmpR, an acronym for di-methyl phenol regulator, for phenol degradation. While DmpR protein has been used in biosensors for detection of  pollutants in environment, the exact mechanism of DmpR activation has puzzled researchers for many years.

A recent study made a breakthrough by solving the molecular structure of the protein, DmpR when bound to phenol. The challenge was overcome by an international team of researchers from three different countries. Scientists from the Korea Research Institute of Bioscience and Biotechnology (KRIBB), South Korea worked together with scientists from the Kavli Institute of Nanoscience Delft, Netherlands and the Department of Molecular Biology, Umea University, Sweden to understand the mechanism of DmpR by solving its phenol-bound crystal structure. This study published in Nature Communications, provides valuable insights into the oligomerization and the signal transduction mechanism of DmpR, which eventually results in degradation of phenolic pollutants.

The team led by Dr. Eui Jeon Woo at the Disease Target Structure Research Center, KRIBB and  Dr. Chirlmin Joo at the Department of Bionanoscience, at the Kavli Institute pioneered the DmpR structural studies advancing the DmpR biosensor technology field. Their discovery of the tetrameric oligomerization state, in contrast to previously thought hexameric state, of the protein helped in understanding its binding to signal transduction factors. The researchers also discovered that protein itself does not utilize energy from hydrolysis of ATP, the cellular currency, to attain oligomeric state but rather directs the energy towards signal transduction and transcriptional activation of proteins involved in the (methyl)phenol-degradative system. With a better understanding of this protein structure and function, highly sensitive whole-cell biosensors can be engineered which can sense and degrade these toxic pollutants. Such sensors can help to prevent accumulation of toxic chemicals that could otherwise cause serious ecological damage as well as contaminate food supplies.  Similarly, DmpR related proteins could also be developed as biosensors that can be used to test different pollutant levels present in the water bodies for protection of the aquatic flora and fauna, thus helping towards preserving ecological niches.

Citation: Park, K., Kim, S., Lee, S. et al. Tetrameric architecture of an active phenol-bound form of the AAA+ transcriptional regulator DmpR. Nat Commun 11, 2728 (2020). https://doi.org/10.1038/s41467-020-16562-5


Arti Dumbrepatil is a science writer. She did her postdoctoral work at the University of Michigan, Ann Arbor, MI, USA. During her tenure at the University of Michigan, she has worked as a Science Communication Fellow (at the Natural History Museum, UMICH) and as a Science Communication Writer (LSA, UMICH). Arti continues to write as a contributing science writer to American Society for Biochemistry and Molecular Biology (ASBMB),Microbiome Digest,Bio Voice News.

Twitter @rtisciwrites