September 13, 2019

In today’s edition, you’ll find a whole new textbook about microbes affecting ecosystem sustainability, reviews about phages and plant viruses, New York Times coverage of clinical trials of FMT for obesity, how to banish “manels” from scientific meetings, and microbiota-related metabolites as biomarkers of aging. Enjoy!

General microbiome
Review: Microbial invasions in terrestrial ecosystems – Madhav P. Thakur – Nature Reviews Microbiology

Preprint: Therapeutically exploring persister metabolism in bacteria – Sayed G. Mohiuddin – bioRxiv

Preprint: Delayed antibiotic exposure induces population collapse in enterococcal communities with drug-resistant subpopulations – Kelsey M Hallinen – bioRxiv

Human gut microbiome
Review: Pairing phages with their hosts in the human gut – Ursula Hofer – Nature Reviews Microbiology

Book chapter: Gut Microbiota and Microbiota-Related Metabolites as Possible Biomarkers of Cognitive Aging – Andrea Ticinesi – Reviews on Biomarker Studies in Aging and Anti-Aging Research

Animal microbiome
Habitat disturbance and the organization of bacterial communities in Neotropical hematophagous arthropods – Kelly L. Bennett – PLOS One

Plant, root, soil microbiome
Book chapter: Rhizospheric Microbiome Engineering as a Sustainable Tool in Agriculture: Approaches and Challenges – Shubham Dubey – Microbial Diversity in Ecosystem Sustainability and Biotechnological Applications

Book chapter: Dynamics of Plant Microbiome and Its Effect on the Plant Traits – Shivali Sharma – Microbial Diversity in Ecosystem Sustainability and Biotechnological Applications

Book chapter: Microbial Diversity of the Sundarbans, the World’s Largest Tidal Mangrove Forest, and Its Bioprospects – Kaushik Biswas – Microbial Diversity in Ecosystem Sustainability and Biotechnological Applications

Water and extremophile microbiome
Capability for arsenic mobilization in groundwater is distributed across broad phylogenetic lineages – Robert E. Danczak – PLOS One

Food microbiology
Book chapter: Microbial Diversity on Grapes and Other Fruits: Role and Significance in Fermentation – M. V. Deshpande – Microbial Diversity in Ecosystem Sustainability and Biotechnological Applications

The Dynamics Analysis of Fungal Community Diversity During the Fermentation Process of Chinese Traditional Soybean Paste – Jingping Ge – Waste and Biomass Valorization

Phages and viruses
Review: Evolution and ecology of plant viruses – Pierre Lefeuvre – Nature Reviews Microbiology

Bioinformatics
An Integrated Approach for Efficient Multi-Omics Joint Analysis – Massimiliano S. Tagliamonte – Proceedings of the 10th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics

Techniques
Polysaccharide-based liquid storage and transport media for non-refrigerated preservation of bacterial pathogens – Janine R. Hutchison – PLOS One

Microbes in the news
Seeking an Obesity Cure, Researchers Turn to the Gut Microbiome -Anahad O’Connor – NY Times

Exclusive: Behind the front lines of the Ebola wars – Amy Maxmen – Nature

Science, publishing, and career
How to banish manels and manferences from scientific meetings – Holly Else – Nature

September 3, 2019

Happy Tuesday and best of luck to those headed back to school! In today’s Digest, you’ll find the virome of the mosquito gut, leveraging blood metabolomics to predict gut alpha diversity, and a comparison of bacterial taxa consumed in organic vs. conventional apples.

General microbiome
Changes in microbial community structure during dark fermentative hydrogen production – Guang Yang – International Journal of Hydrogen Energy

Pregnancy and early life
Effect of the vaginal microbiome on the pregnancy rate in women receiving assisted reproductive treatment – Andrea Bernabeu – Journal of Assisted Reproduction and Genetics

Maturation of the infant rhesus macaque gut microbiome and its role in the development of diarrheal disease – Nicholas Rhoades – Genome Biology

Human gut microbiome
Blood metabolome predicts gut microbiome α-diversity in humans – Nature Biotechnology – Tomasz Wilmanski

B cell superantigens in the human intestinal microbiota – Jeffrey J. Bunker – Science Translational Medicine

Long-read metagenomic exploration of extrachromosomal mobile genetic elements in the human gut – Yoshihiko Suzuki – Microbiome

Microbiome of death
Preprint: Manner of death and demographic effects on microbial community composition in organs of the human cadaver – Holly L Lutz – bioRxiv

Animal experiments
Diet-induced remission in chronic enteropathy is associated with altered microbial community structure and synthesis of secondary bile acids – Shuai Wang – Microbiome

Animal microbiome
Testing the relationship between microbiome composition and flux of carbon and nutrients in Caribbean coral reef sponges – Shelby E. Gantt – Microbiome

Plant, root, and soil microbiome
A new family of uncultivated bacteria involved in methanogenesis from the ubiquitous osmolyte glycine betaine in coastal saltmarsh sediments – Helen J. Jones – Microbiome

Top-down Enrichment Guides in Formation of Synthetic Microbial Consortia for Biomass Degradation – Sean P. Gilmore – ACS Synthetic Biology

Microbial community response to environmental changes in a technosol historically contaminated by the burning of chemical ammunitions – Hugues Thouin – Science of the Total Environment

Preprint: Intra-genus metabolic diversity facilitates co-occurrence of multiple Ferrovum species at an acid mine drainage site – Christen L Grettenberger – bioRxiv

Water and extremophile microbiome
Exploring the effects of operational mode and microbial interactions on bacterial community assembly in a one-stage partial-nitritation anammox reactor using integrated multi-omics – Yulin Wang – Microbiome

Fungi in salterns – Dawoon Chung – Journal of Microbiology

Distinct temporal dynamics of planktonic archaeal and bacterial assemblages in the bays of the Yellow Sea – Jong-Geol Kim – Plos One

Food microbiology
An Apple a Day: Which Bacteria Do We Eat With Organic and Conventional Apples? – Birgit Wassermann – Frontiers in Microbiology

Preprint: Molecular characterization of bacterial communities in sheep cheese through 16S rRNA gene sequencing – Creciana Maria Endres – bioRxiv

Phages and viruses
Stable distinct core eukaryotic viromes in different mosquito species from Guadeloupe, using single mosquito viral metagenomics – Chenyan Shi – Microbiome

The virome of cerebrospinal fluid: viruses where we once thought there were none – Chandrabali Ghose – Frontiers in Microbiology

Detecting viral sequences in NGS data – Paul G. Cantalupo – Current Opinion in Virology

Bioinformatics
Identification of discriminatory antibiotic resistance genes among environmental resistomes using extremely randomized tree algorithm – Suraj Gupta – Microbiome

June 24, 2019

Happy Monday! In today’s Digest, you’ll find a primer on metabolomics, a description of the fungal and bacterial communities involved in coffee fermentation, and several studies on extremophile communities.

General Microbiome
Staring into the void: Demystifying microbial metabolomics – Cynthia M Grim – FEMS Microbiology Letters

Bacterial metabolism-inspired molecules to modulate antibiotic efficacy – Yuan Liu – Journal of Antimicrobial Chemotherapy

Deterministic processes structure bacterial genetic communities across an urban landscape – J. M. Hassell – Nature Communications

Gut Microbiome
Bifidobacterium dentium Fortifies the Intestinal Mucus Layer via Autophagy and Calcium Signaling Pathways – Melinda A. Engevik – mBio

Lipopolysaccharides modulate intestinal epithelial permeability and inflammation in a species-specific manner – Matthew Stephens – Gut Microbes

Fecal Microbiome Data Distinguish Liver Recipients with Normal and Abnormal Liver Function from Healthy Controls – Hai-feng Lu – Frontiers in Microbiology

Human Microbiota and Personalized Cancer Treatments: Role of Commensal Microbes in Treatment Outcomes for Cancer Patients – Stephen Gately – Precision Medicine in Cancer Therapy

Animal Experiments
Intervening Effects of Total Alkaloids of Corydalis saxicola Bunting on Rats With Antibiotic-Induced Gut Microbiota Dysbiosis Based on 16S rRNA Gene Sequencing and Untargeted Metabolomics Analyses – Xi Liu – Frontiers in Microbiology

Animal Microbiome
Gestation alters the gut microbiota of an oviparous lizard – Brian K Trevelline – FEMS Microbiology Ecology

Diversity of deep-water coral associated bacteria and comparison across depth gradients – Sigmund Jensen – FEMS Microbiology Ecology

Plant, Root, and Soil Microbiome
Bacterial and archaeal spatial distribution and its environmental drivers in an extremely haloalkaline soil at the landscape scale – Martha Adriana Martínez-Olivas – PeerJ

The microbial community in an alkaline saline sediment of a former maar lake bed – Claudia L. Ibarra-Sánchez – Journal of Soils and Sediments

Impacts on soil microbial characteristics and their restorability with different soil disinfestation approaches in intensively cropped greenhouse soils – Tianzhu Meng – Applied Microbiology and Biotechnology

Nonylphenol causes shifts in microbial communities and nitrogen mineralization in soil microcosms – Stefania Mattana – Ecotoxicology and Environmental Safety

Changes in Plant Rhizosphere Microbial Communities under Different Vegetation Restoration Patterns in Karst and Non-karst Ecosystems – Zhouzhou Fan – Scientific Reports

Water and Extremophile Microbiome
Culture independent bacterial diversity of Changme Khang and Changme Khangpu glaciers of North Sikkim, India – Mingma Thundu Sherpa – Environmental Sustainability

Selection of a Microbial Community in the Course of Formation of Acid Mine Drainage – V. V. Kadnikov – Microbiology

Thermophilic Bacteria in Lake Baikal Bottom Sediments Associated with Hydrocarbon Discharge – O. N. Pavlova – Microbiology

Bacterial alkylquinolone signaling contributes to structuring microbial communities in the ocean – Kristen E. Whalen – Microbiome

Food Microbiology
First description of bacterial and fungal communities in Colombian coffee beans fermentation analysed using Illumina-based amplicon sequencing – Ana C. de Oliveira Junqueira – Scientific Reports

Techniques
Functional Gene Array-Based Ultrasensitive and Quantitative Detection of Microbial Populations in Complex Communities – Zhou Shi – mSystems

June 4, 2019

General microbiome
Rigorous Statistical Methods for Rigorous Microbiome Science – Amy D. Willis – mSystems

Understanding microbial community dynamics to improve optimal microbiome selection – Robyn J. Wright – Microbiome

Toward a Better Understanding of Species Interactions through Network Biology – Ryan S. McClure – mSystems

Human respiratory microbiome
Nasal commensal Staphylococcus epidermidis enhances interferon-λ-dependent immunity against influenza virus – Hyun Jik Kim – Microbiome

Human gut microbiome
A Multi-omics Approach to Unraveling the Microbiome-Mediated Effects of Arabinoxylan Oligosaccharides in Overweight Humans – Alfonso Benítez-Páez – mSystems

Gut microbiome identifies risk for colorectal polyps – Ezzat Dadkhah – BMJ Open Gastroenterology

Yogurt improves insulin resistance and liver fat in obese women with nonalcoholic fatty liver disease and metabolic syndrome: a randomized controlled trial – Yang Chen – American Journal of Clinical Nutrition

Preprint: Chemical Impacts of the Microbiome Across Scales Reveal Novel Conjugated Bile Acids – Robert A Quinn – bioRxiv

Animal models
Ruminal microbiome-host crosstalk stimulates the development of the ruminal epithelium in a lamb model – Limei Lin – Microbiome

Missing Links: the Role of Primates in Understanding the Human Microbiome – Katherine R. Amato – mSystems

Plant, root, and soil microbiome
Collaborative involvement of woody plant roots and rhizosphere microorganisms in the formation of pedogenetic clays – Frank Reith – Annals of Botany

Water and extremophile microbiome
Effects of sulfamethoxazole and sulfamethoxazole-degrading bacteria on water quality and microbial communities in milkfish ponds – Bea-Ven Chang – Environmental Pollution

Preprint: Temporal dynamics of Bacteria, Archaea and protists in equatorial coastal waters – Caroline Chénard – bioRxiv

Built environment
Concurrent measurement of microbiome and allergens in the air of bedrooms of allergy disease patients in the Chicago area – Miles Richardson – Microbiome

Phages and viruses
Preprint: The human gut virome is highly diverse, stable and individual-specific – Andrey Shkoporov – bioRxiv

Bioinformatics
NG-meta-profiler: fast processing of metagenomes using NGLess, a domain-specific language – Luis Pedro Coelho – Microbiome

Science, publishing, and career
Preprint: The Mastery Rubric for Bioinformatics: supporting design and evaluation of career-spanning education and training – Rochelle E. Tractenberg – bioRxiv

Alyson’s non-microbiology picks
Why Your Metro Commute Is So Insanely Windy – Julie Bogen – The Atlantic

The 2019 Wellcome photography prize: close focus on the human condition – Sean O’Hagan – The Guardian

May 22, 2019

Today’s Digest is full of new perspectives on appropriate models and techniques, including the future of gnotobiotics and using unbiased metagenomics to find RNA viruses. There are also several plant, root, and soil papers, particularly examining the interplay between bacterial and fungal communities. Finally, enjoy a preprint about the cartography of antibiotic resistance genes in a hospital, a study examining the microbiota in larval mosquito vectors of malaria, and a paper about the microeukaryotes associated with coral reefs.

General Microbiome
Review: Antibiotics versus biofilm: an emerging battleground in microbial communities – Divakar Sharma – Antimicrobial Resistance & Infection Control

Review: Gnotobiotics: Past, present and future – Marijana Basic – Laboratory Animals

Review: The use of non-rodent model species in microbiota studies – Aaron C. Ericsson – Laboratory Animals

Pregnancy and Early Life
Influence of a Serratia marcescens outbreak on the gut microbiota establishment process in low-weight preterm neonates – Esperanza Escribano – PLoS One

Human Vaginal Microbiome
Vaginal microbiota and mucosal pharmacokinetics of tenofovir in healthy women using tenofovir and tenofovir/levonorgestrel vaginal rings – Andrea Ries Thurman – PLoS One

Human Oral Microbiome
Aerodigestive sampling reveals altered microbial exchange between lung, oropharyngeal, and gastric microbiomes in children with impaired swallow function – Claire Duvallet – PLoS One

Animal Microbiome
Color morphology of Diaphorina citri influences interactions with its bacterial endosymbionts and ‘Candidatus Liberibacter asiaticus’ – Saeed Hosseinzadeh – PLoS One

Conspecific coprophagy stimulates normal development in a germ-free model invertebrate – Benjamin C. Jahnes – PeerJ

Malaria vector species in Amazonian Peru co-occur in larval habitats but have distinct larval microbial communities – Catharine Prussing – PLoS Neglected Tropical Diseases

Animal Experiments
Gut and immune effects of bioactive milk factors in preterm pigs exposed to prenatal inflammation – Shuqiang Ren – American Journal of Physiology-Gastrointestinal and Liver Physiology

Effects of oregano essential oil on the ruminal pH and microbial population of sheep – Rui Zhou – PLoS One

Plant, Root, and Soil Microbiome
Characterizing the intra-vineyard variation of soil bacterial and fungal communities – Hebin Liang – Frontiers in Microbiology

The role of fungi in heterogeneous sediment microbial networks – Jenny Marie Booth – Scientific Reports

Altering N2O emissions by manipulating wheat root bacterial community – Alla Usyskin-Tonne – Scientific Reports

Sphingomonas sp. Cra20 Increases Plant Growth Rate and Alters Rhizosphere Microbial Community Structure of Arabidopsis Thaliana Under Drought Stress – Yang Luo – Frontiers in Microbiology

Enrichment of soil rare bacteria in root by an invasive plant Ageratina adenophora – Lin Chen – Science of the Total Environment

Effect of rhizospheric and endophytic bacteria with multiple plant growth promoting traits on wheat growth – Somayeh Emami – Environmental Science and Pollution Research

Water and Extremophile Microbiome
A comparison of microeukaryote communities inhabiting sponges and seawater in a Taiwanese coral reef system – Daniel Francis Richard Cleary – Annals of Microbiology

An integrated insight into the response of bacterial communities to anthropogenic contaminants in a river: A case study of the Wonderfonteinspruit catchment area, South Africa – K. Jordaan – PLoS One

Built Environment
Preprint: Cartography of opportunistic pathogens and antibiotic resistance genes in a tertiary hospital environment – Kern Rei Chng – bioRxiv

Fungal community composition analysis of 24 different urban parks in Shanghai, China – Jing Zhang – Urban Ecosystems

Techniques
Expanding the RNA Virosphere by Unbiased Metagenomics – Yong-Zhen Zhang – Annual Review of Virology

Preprint: Next-generation sequencing of double stranded RNA is greatly improved by treatment with the inexpensive denaturing reagent DMSO – Alexander H. Wilcox – bioRxiv

Development of an autonomous biosampler to capture in situ aquatic microbiomes – Hugo Ribeiro – PLoS One

March 21, 2019

Happy Spring! Today’s Digest features a megaphylogeny of mushrooms, new papers about the respiratory microbiome, fecal microbiome and metatranscriptomic analysis from nonhuman primates, and the microbial ecology of snow. Bonus: a pick about the first woman to win the Abel Prize.

General Microbiome
Megaphylogeny resolves global patterns of mushroom evolution – Torda Varga – Nature Ecology and Evolution

Fate of CMY-2-encoding plasmids introduced into the human fecal microbiota by exogenous Escherichia coli – Mehreen Anjum – Antimicrobial Agents and Chemotherapy

Review: The impact of indigenous microbes on Parkinson’s disease – Timothy Sampson – Neurobiology of Disease

Pregnancy and Early Life
Michigan cohorts to determine associations of maternal pre-pregnancy body mass index with pregnancy and infant gastrointestinal microbial communities: Late pregnancy and early infancy – Kameron Y. Sugino – PLOS One

Human Respiratory Microbiome
Bacterial and viral respiratory tract microbiota and host characteristics in children with lower respiratory tract infections: a matched case-control study – Wing Ho Man – The Lancet Respiratory Medicine

The Yin and Yang of Streptococcus Lung Infections in Cystic Fibrosis: A Model for Studying Polymicrobial Interactions – Jessie E. Scott – Journal of Bacteriology

The nasal and oropharyngeal microbiomes of healthy livestock workers – Ashley E. Kates – PLOS One

Human Gut Microbiome
Review: Role of SCFAs in gut microbiome and glycolysis for colorectal cancer therapy – Gang Wang – Journal of Cellular Physiology

Review: Obesity, Motility, Diet, and Intestinal Microbiota—Connecting the Dots – Maya Fayfman – Current Gastroenterology Reports

Review: The gut microbiome and response to immune checkpoint inhibitors: preclinical and clinical strategies – Jun Gong – Clinical and Translational Medicine

The exosome secretion inhibitor neticonazole suppresses intestinal dysbacteriosis-induced tumorigenesis of colorectal cancer – Lei Gu – Investigational New Drugs

Glutamate interactions with obesity, insulin resistance, cognition and gut microbiota composition – María Encarnación Palomo-Buitrago – Acta Diabetologica

Understanding the gut–kidney axis among biopsy-proven diabetic nephropathy, type 2 diabetes mellitus and healthy controls: an analysis of the gut microbiota composition – Sibei Tao – Acta Diabetologica

Identification of the microbial diversity after fecal microbiota transplantation therapy for chronic intractable constipation using 16s rRNA amplicon sequencing – Tadashi Ohara – PLOS One

Animal Experiments
Gut microbiota from infant with Cow’s Milk Allergy promotes clinical and immune features of atopy in a murine model – A. Mauras – Allergy

N-(1-carbamoyl-2-phenylethyl) butyramide reduces antibiotic-induced intestinal injury, innate immune activation and modulates microbiota composition – Adriano Lama – Scientific Reports

Immunosuppression-induced alterations in fish gut microbiota may increase the susceptibility to pathogens – Xiao-Zhou Qi – Fish & Shellfish Immunology

Rifaximin Alters Intestinal Microbiota and Prevents Progression of Ankylosing Spondylitis in Mice – Lianjun Yang – Frontiers in Cellular and Infection Microbiology

Hydroxytyrosol Improves Obesity and Insulin Resistance by Modulating Gut Microbiota in High-Fat Diet-Induced Obese Mice – Zhuoqun Liu – Frontiers in Microbiology

Review: Dietary Fiber and Intestinal Health of Monogastric Animals – Rajesh Jha – Frontiers in Veterinary Science

Circadian disruption and divergent microbiota acquisition under extended photoperiod regimens in chicken – Anne-Sophie Charlotte Hieke – PeerJ

Animal Microbiome
Fecal metatranscriptomics of macaques with idiopathic chronic diarrhea reveals altered mucin degradation and fucose utilization – Samuel T. Westreich – Microbiome

Microbiome Profiles of Ligature-Induced Periodontitis in Nonhuman Primates Across the Lifespan – Sreenatha Kirakodu – Infection and Immunity

Diabetic cats have decreased gut microbial diversity and a lack of butyrate producing bacteria – Ida Nordang Kieler – Scientific Reports

Exploring the bacteriome in anthropophilic ticks: To investigate the vectors for diagnosis – Aránzazu Portillo – PLOS One

Plant, Root, and Soil Microbiome
Microbiota in Non-flooded and Flooded Rice Culms – Hui-Ling Cui – FEMS Microbiology Ecology

Microbial community structure in full scale anaerobic mono-and co-digesters treating food waste and animal waste – Taewoan Koo – Bioresource Technology

Variations in pH significantly affect cadmium uptake in grafted muskmelon (Cucumis melo L.) plants and drive the diversity of bacterial communities in a seedling substrate – Jian Zhang – Plant Physiology and Biochemistry

Divergent microbial communities in groundwater and overlying soils exhibit functional redundancy for plant-polysaccharide degradation – Martin Taubert – PLOS One

Microbial diversity and soil physiochemical characteristic of higher altitude – Saurabh Kumar – PLOS One

Water and Extremophile Microbiome
Microbial Ecology of Snow Reveals Taxa-Specific Biogeographical Structure – Shawn P. Brown – Microbial Ecology

Bacterial community in cold and alkaline environments of Hoh Xil basin in Qinghai–Tibet Plateau and isolation of potential sources of microbiota – Rui Xing – Annals of Microbiology

Bacterial communities of the microbial mats of Chokrak sulfide springs – Ekaterina I. Burganskaya – Archives of Microbiology

Dynamics of microbial community in the bioreactor for bisphenol S removal – Wen-Cong Huang – Science of the Total Environment

High-throughput DNA sequencing reveals the dominance of pico- and other filamentous cyanobacteria in an urban freshwater Lake – Hanyan Li – Science of the Total Environment

A novel phenol and ammonia recovery process for coal gasification wastewater altering the bacterial community and increasing pollutants removal in anaerobic/anoxic/aerobic system – Xuefei Gui – Science of the Total Environment

Built Environment
Biodeterioration of mortar coating in historical buildings: Microclimatic characterization, material, and fungal community – Fernanda L. Guerra – Building and Environment

A different suite: The assemblage of distinct fungal communities in water-damaged units of a poorly-maintained public housing building – Iman A. Sylvain – PLOS One

Microbes in Space
Subsurface Microbial Habitats in an Extreme Desert Mars-Analog Environment – Kimberley A. Warren-Rhodes – Frontiers in Microbiology

Food Microbiology
Microbiome patterns reveal the transmission of pathogenic bacteria in hilsa fish (Tenualosa ilisha) marketed for human consumption in Bangladesh – Md Javed Foysal – Journal of Applied Microbiology

Impact of turning, pod storage and fermentation time on microbial ecology and volatile composition of cocoa beans – Yasmine Hamdouche – Food Research International

Probiotic potential of a Lactobacillus rhamnosus cheese isolate and its effect on the fecal microbiota of healthy volunteers – Joaquin Bautista-Gallego – Food Research International

Dynamics of biogenic amines and bacterial communities in a Thai fermented pork product Nham – Pannita Santiyanont – Food Research International

Probiotics/Prebiotics
16S rRNA gene profiling and genome reconstruction reveal community metabolic interactions and prebiotic potential of medicinal herbs used in neurodegenerative disease and as nootropics – Christine Tara Peterson – PLOS One

Phages and Viruses
Review: Phage therapy: What factors shape phage pharmacokinetics and bioavailability? Systematic and critical review – Krystyna Dąbrowska – Medicinal Research Reviews

Bioinformatics
MetaPheno: A Critical Evaluation of Deep Learning and Machine Learning in Metagenome-Based Disease Prediction – Nathan LaPierre – Methods

Assessing alignment-based taxonomic classification of ancient microbial DNA – Raphael Eisenhofer – PeerJ

Techniques
A comparison of storage methods for gut microbiome studies in teleosts: Insights from rainbow trout (Oncorhynchus mykiss) – Mathis Hildonen – Journal of Microbiological Methods

Alyson’s Non-Microbiology Picks
Soap-bubble pioneer is first woman to win prestigious maths prize

Girls who share a womb with boys tend to make less money than those with twin sisters

 

March 11, 2019

To start off the week, here’s a rundown of new papers, including how symbiotic Vibrio signals drive squid gene expression, the intergenerational fur seal microbiome, and a few food microbiology studies on kimchi and pasta. Happy reading!

Pregnancy and Early Life
Review: Neonatal microbiome – a brief review – Anchala Singh – The Journal of Maternal-Fetal & Neonatal Medicine

Feeding practice influences gut microbiome composition in very low birth weight preterm infants and the association with oxidative stress: A prospective cohort study – Chenxi Cai – Free Radical Biology and Medicine

Human Skin Microbiome
Commensal Staphylococci Influence Staphylococcus aureus Skin Colonization and Disease – Corey P. Parlet – Trends in Microbiology

Human Oral Microbiome
No differences in microbiome changes between anti-adhesive and antibacterial ingredients in toothpastes during periodontal therapy – Daniel Hagenfeld – Journal of Periodontal Research

Human Gut Microbiome
Endocytosis of commensal antigens by intestinal epithelial cells regulates mucosal T cell homeostasis – Mark S. Ladinsky – Science

Review: Mendelian randomization reveals causal effects of the gut microbiota – Hugh Thomas – Nature Reviews Gastroenterology & Hepatology

Association Between Antibiotics in the First Year of Life and Celiac Disease – Stine Dydensborg Sander – Gastroenterology

Daiokanzoto (Da-Huang-Gan-Cao-Tang) is an effective laxative in gut microbiota associated with constipation – Kento Takayama – Scientific Reports

Dietary raisin intake has limited effect on gut microbiota composition in adult volunteers – Akemi T. Wijayabahu – Nutrition Journal

Early gut microbiota signature of aGvHD in children given allogeneic hematopoietic cell transplantation for hematological disorders – Elena Biagi – BMC Medical Genomics

Fecal Calprotectin and Fecal Indole Predicts Outcome of Fecal Microbiota Transplantation in Subjects with Recurrent Clostridium difficile Infection – J. Hibbard – Anaerobe

Gut microbiota-stimulated cathepsin K secretion mediates TLR4-dependent M2 macrophage polarization and promotes tumor metastasis in colorectal cancer – Rui Li – Cell Death & Differentiation

Alterations in bacterial communities, SCFA and biomarkers in an elderly HIV-positive and HIV-negative population in western Mexico – Luz A. González-Hernández – BMC Infectious Diseases

RA and the microbiome: do host genetic factors provide the link? – Philippa M. Wells – Journal of Autoimmunity

The Gut Microbiota in Causation, Detection, and Treatment of Cancer – Clodagh Murphy – The American Journal of Gastroenterology

Gut-Brain Axis
From Infection to the Microbiome: An Evolving Role of Microbes in Schizophrenia – Emily G. Severance – Current Topics in Behavioral Neurosciences

Animal Experiments
Critical symbiont signals drive both local and systemic changes in diel and developmental host gene expression – Silvia Moriano-Gutierrez – PNAS

Different host-specific responses in thyroid function and gut microbiota modulation between diet-induced obese and normal mice given the same dose of iodine – Huiting Shen – Applied Microbiology and Biotechnology

Antibiotic treatment affects the expression levels of copper transporters and the isotopic composition of copper in the colon of mice – Kerri A. Miller – PNAS

Protective effect of prebiotic and exercise intervention on knee health in a rat model of diet-induced obesity – Jaqueline Lourdes Rios – Scientific Reports

Chlorogenic acid alleviates obesity and modulates gut microbiota in high-fat-fed mice – Zhengyu Wang – Food Science & Nutrition

Crucial Role of Microbiota in Experimental Psoriasis Revealed by a Gnotobiotic Mouse Model – Zuzana Stehlikova – Frontiers in Microbiology

Parasitoid envenomation alters the Galleria mellonella midgut microbiota and immunity, thereby promoting fungal infection – Olga V. Polenogova – Scientific Reports

Nutritional Interventions Improved Rumen Functions and Promoted Compensatory Growth of Growth-Retarded Yaks as Revealed by Integrated Transcripts and Microbiome Analyses – Rui Hu – Frontiers in Microbiology

Animal Microbiome
Fur seal microbiota are shaped by the social and physical environment, show mother-offspring similarities and are associated with host genetic quality – Stefanie Grosser – Molecular Ecology

Intensity of Nosema ceranae infection is associated with specific honey bee gut bacteria and weakly associated with gut microbiome structure – Andrey Rubanov – Scientific Reports

Characterizing the microbiota in gastrointestinal tract segments of Rhabdophis subminiatus: Dynamic changes and functional predictions – Wenjiao Tang – MicrobiologyOpen

Studying the microbiota of bats: Accuracy of direct and indirect samplings – Muriel Dietrich – Ecology and Evolution

A cellulolytic fungal biofilm enhances the consolidated bioconversion of cellulose to short chain fatty acids by the rumen microbiome – Charilaos Xiros – Applied Microbiology and Biotechnology

Plant, Root, and Soil Microbiome
Changes in the soil microbial community are associated with the occurrence of Panax quinquefolius L. root rot diseases – Jinglong Jiang – Plant and Soil

Metagenomic analysis reveals distinct patterns of denitrification gene abundance across soil moisture, nitrate gradients – Sarah A. Nadeau – Environmental Microbiology

Divergent national-scale trends of microbial and animal biodiversity revealed across diverse temperate soil ecosystems – Paul B. L. George – Nature Communications

Impact of Wuyiencin Application on the Soil Microbial Community and Fate of Typical Antibiotic Resistance Genes – Liming Shi – Scientific Reports

Airborne microbial transport limitation to isolated Antarctic soil habitats – Stephen D. J. Archer – Nature Microbiology

Agricultural intensification reduces microbial network complexity and the abundance of keystone taxa in roots – Samiran Banerjee – ISMEJ

Biochars reduced the bioaccessibility and (bio)uptake of organochlorine pesticides and changed the microbial community dynamics in agricultural soils -Neelum Ali – Chemosphere

Molecular identification and biocontrol activity of sugarcane rhizosphere bacteria against red rot pathogen Colletotrichum falcatum – Prittesh Patel – Biotechnology Reports

Natural and assisted dissipation of polycyclic aromatic hydrocarbons in a long-term co-contaminated soil with creosote and potentially toxic elements
F.Madrid – Science of The Total Environment

Horizontal gene transfer and shifts in linked bacterial community composition are associated with maintenance of antibiotic resistance genes during food waste composting – Hanpeng Liao – Science of The Total Environment

Sedimentary Marl mudstone as a substrate in a xeric environment revealed by microbiome analysis – Oksana Koryachenko – Extremophiles

Water and Extremophile Microbiome
Drivers of Regional Bacterial Community Structure and Diversity in the Northwest Atlantic Ocean – Jackie Zorz – Frontiers in Microbiology

Microbial community composition in alpine lake sediments from the Hengduan Mountains – Binqiang Liao – MicrobiologyOpen

Stepwise pH control to promote synergy of chemical and biological processes for augmenting short-chain fatty acid production from anaerobic sludge fermentation – Xu Wang – Water Research

Food Microbiology
Effects of the supplementation of plant-based formulations on microbial fermentation and predicted metabolic function in vitro – Renée Maxine Petri – Anaerobe

Effects of functional pasta ingredients on different gut microbiota as revealed by TIM-2 in vitro model of the proximal colon – A. Martina – Beneficial Microbes

Effect of pasteurization on delayed kimchi ripening and regression analysis for shelf life estimation of kimchi – Hyun‐Gyu Lee – Food Science & Nutrition

Optimization on production of konjac oligo‐glucomannan and their effect on the gut microbiota – Catarina Aprilia Ariestanti – Food Science & Nutrition

Probiotics
Mechanisms and immunomodulatory properties of pre- and probiotics – V.B.M. Peters – Beneficial Microbes

Wild bacterial probiotics fed to larvae of mass-reared Queensland fruit fly [Bactrocera tryoni (Froggatt)] do not impact long-term survival, mate selection or locomotor activity – Lucas A. Shuttleworth – Insect Science

Bioinformatics
Web-gLV: A Web Based Platform for Lotka-Volterra Based Modeling and Simulation of Microbial Populations – Bhusan K. Kuntal – Frontiers in Microbiology

Techniques
PCR effects of melting temperature adjustment of individual primers in degenerate primer pools – Ankur Naqib -PeerJ

Review: Combinatory biotechnological intervention for gut microbiota – Ishu Khangwal – Applied Microbiology and Biotechnology

March 8, 2019

Happy Friday! Read on for insights into the relationship between the oral microbiome and taste perception, how earthworms interact with pathogens during vermicomposting, the use of phages against drug resistant bacterial pathogens, and how microbiota depletion affects brown adipose tissue thermogenesis. Plus, two new techniques for shotgun metagenomes.

General microbiome
Quorum Sensing Signal Selectivity and the Potential for Interspecies Cross Talk – Samantha Wellington – mBio

Streptomyces Volatile Compounds Influence Exploration and Microbial Community Dynamics by Altering Iron Availability – Stephanie E. Jones – mBio

Microbiome Imbalances: An Overlooked Potential Mechanism in Chronic Nonhealing Wounds – Mengru Pang – The International Journal of Lower Extremity Wounds

Human oral microbiome
New insights into the relationship between taste perception and oral microbiota composition – Camilla Cattaneo – Scientific Reports

The Supragingival Biofilm in Early Childhood Caries: Clinical and Laboratory Protocols and Bioinformatics Pipelines Supporting Metagenomics, Metatranscriptomics, and Metabolomics Studies of the Oral Microbiome – Kimon Divaris – Odontogenesis

Human vaginal microbiome
Comparison of the Vaginal Microbiomes of Premenopausal and Postmenopausal Women – Karol Gliniewicz – Frontiers in Microbiology

Pregnancy and early life
Dose-interval study of a dual probiotic in preterm infants – Claire Watkins – Archives of Disease in Childhood – Fetal and Neonatal Edition

Review: The Relationship Between Perinatal Mental Health and Stress: a Review of the Microbiome – Nusiebeh Redpath – Current Psychiatry Reports

Multi-site human microbiome
Preprint: Functional metagenomics-guided discovery of potent Cas9 inhibitors in the human microbiome – Kevin J Forsberg – bioRxiv

Human gut microbiome
Infectious Complications Are Associated With Alterations in the Gut Microbiome in Pediatric Patients With Acute Lymphoblastic Leukemia – Jacob T Nearing – Frontiers in Cellular and Infection Microbiology

Preprint: HLA alleles associated with risk of ankylosing spondylitis and rheumatoid arthritis influence the gut microbiome – Mark Asquith – bioRxiv

Preprint: Gut feelings begin in childhood: how the gut metagenome links to early environment, caregiving, and behavior – Jessica Flannery – bioRxiv

Review: From gut microbiota dysfunction to obesity: could short-chain fatty acids stop this dangerous course? – Luigi Barrea – Hormones

Animal microbiome
Microbial communities in hummingbird feeders are distinct from floral nectar and influenced by bird visitation – Casie Lee – Proceedings of the Royal Society B

High individual variability in the transcriptomic response of Mediterranean mussels to Vibrio reveals the involvement of myticins in tissue injury – Magalí Rey-Campos – Scientific Reports

The Bos taurus maternal microbiome: Role in determining the progeny early-life upper respiratory tract microbiome and health – Svetlana Ferreira Lima – PLoS One

Contact with adult hen affects development of caecal microbiota in newly hatched chicks – Tereza Kubasova – PLoS One

Examination of the temporal and spatial dynamics of the gut microbiome in newborn piglets reveals distinct microbial communities in six intestinal segments – Ying Liu – Scientific Reports

Microbial diversity in the tick Argas japonicus (Acari: Argasidae) with a focus on Rickettsia pathogens – P. Yan – Medical and Veterinary Entomology

Mutual interactions of E. andrei earthworm and pathogens during the process of vermicomposting – Radka Roubalová – Environmental Science and Pollution Research

Animal experiments
Microbiota Depletion Impairs Thermogenesis of Brown Adipose Tissue and Browning of White Adipose Tissue – Baoguo Li – Cell Reports

Fasting-Mimicking Diet Modulates Microbiota and Promotes Intestinal Regeneration to Reduce Inflammatory Bowel Disease Pathology – Priya Rangan – Cell Reports

Linseed oil and heated linseed grain supplements have different effects on rumen bacterial community structures and fatty acid profiles in cashmere kids – Xue Wang – Journal of Animal Science

Sodium butyrate supplementation in high-soybean meal diets for turbot (Scophthalmus maximus L.): Effects on inflammatory status, mucosal barriers and microbiota in the intestine – Yang Liu – Fish and Shellfish Immunology

The gut microbiota composition affects dietary polyphenols-mediated cognitive resilience in mice by modulating the bioavailability of phenolic acids – Tal Frolinger – Scientific Reports

Dietary lysozyme supplementation contributes to enhanced intestinal functions and gut microflora of piglets – Xia Xiong – Food and Function

Plant, root, and soil microbiome
Potential role of weather, soil and plant microbial communities in rapid decline of apple trees – Jugpreet Singh – PLoS One

The structure of denitrifying microbial communities in constructed mangrove wetlands in response to fluctuating salinities – Guiping Fu – Journal of Environmental Management

Exploring the links between bacterial communities and magnetic susceptibility in bulk soil and rhizosphere of beech (Fagus sylvatica L.) – Carolina Chiellini – Applied Soil Ecology

Impact of Fabricated Nanoparticles on the Rhizospheric Microorganisms and Soil Environment – Mokula Mohammed Raffi – Nanomaterials and Plant Potential

Variation in soil fungal community structure during successive rotations of Casuarina equisetifolia plantations as determined by high-throughput sequencing analysis – Zhou Liuting – Plant Growth Regulation

Water and extremophile microbiome
Microbial responses to anthropogenic dissolved organic carbon in Arctic and Antarctic coastal seawaters – Elena Cerro‐Gálvez – Environmental Microbiology

Microbes in Space
A Low-Diversity Microbiota Inhabits Extreme Terrestrial Basaltic Terrains and Their Fumaroles: Implications for the Exploration of Mars – Charles S. Cockell – Astrobiolgy

Phages and Viruses
Targeting antibiotic resistant bacteria with phage reduces bacterial density in an insect host – Lauri Mikonranta – Biology Letters

Bioinformatics
Autometa: automated extraction of microbial genomes from individual shotgun metagenomes – Ian J Miller – Nucleic Acids Research

Preprint: Toward perfect reads: short reads correction via mapping on compacted de Bruijn graphs – Antoine Limasset – bioRxiv

 

January 15, 2019

Highlights today include the organisms in the healthy infant intestinal microbiome that protect against food allergy, an algorithm to predict aging based on the gut microbiome, and how bacteria adapt to life on the International Space Station. Enjoy!

Pregnancy and early life
Healthy infants harbor intestinal bacteria that protect against food allergy – Taylor Feehley – Nature Medicine

Human gut microbiome
Preprint: Human microbiome aging clocks based on deep learning and tandem of permutation feature importance and accumulated local effects – Fedor Galkin – bioRxiv
(Covered in popular press as Your Gut Microbiome Could Actually Reveal Your Age, Study Shows)

Preprint: The virome in adult monozygotic twins with concordant or discordant gut microbiomes – J. Leonardo Moreno-Gallego – bioRxiv

Human nearly-sterile sites
Review: Microbiome–metabolome reveals the contribution of gut–kidney axis on kidney disease – Yuan-Yuan Chen – Journal of Translational Medicine

Animal experiments
Lactobacillus sakei Alleviates High-fat Diet-induced Obesity and Anxiety in Mice by Inducing AMPK Activation and SIRT1 Expression and Inhibiting Gut Microbiota-mediated NF-κB Activation – Hyo-Min Jang – Molecular Nutrition and Food Research

Aqueous raw and ripe Pu-erh tea extracts alleviate obesity and alter cecal microbiota composition and function in diet-induced obese rats – Yun Xia – Applied Microbiology and Biotechnology

Impact of intramammary inoculation of inactivated Lactobacillus rhamnosus and antibiotics on the milk microbiota of water buffalo with subclinical mastitis – Carlotta Catozzi – PLOS One

Plant, root, and soil microbiome
Superior dispersal ability can lead to persistent ecological dominance throughout succession – Primrose J. Boynton – Applied and Environmental Microbiology

Plant growth-promoting rhizobacterium Pseudomonas PS01 induces salt tolerance in Arabidopsis thaliana – Thanh Nguyen Chu – BMC Research Notes

Diversity analysis of the rhizospheric and endophytic bacterial communities of Senecio vulgaris L. (Asteraceae) in an invasive range – Dandan Cheng – PeerJ\

Antifungal potential of bacterial rhizosphere isolates associated with three ethno-medicinal plants (poppy, chamomile, and nettle) – Marija Mojicevic – International Microbiology

Analysis of uranium removal capacity of anaerobic granular sludge bacterial communities under different initial pH conditions – Taotao Zeng – Environmental Science and Pollution Research

Water and extremophile microbiomes
An interspecies malate–pyruvate shuttle reconciles redox imbalance in an anaerobic microbial community – Po-Hsiang Wang – The ISME Journal

Bacterial community assembly in a typical estuarine marsh with multiple environmental gradients – Zhiyuan Yao – Applied and Environmental Microbiology

Effects of salinity on microbialite-associated production in Great Salt Lake, Utah – Melody R. Lindsay – Ecology

Preprint: Capturing the Diversity of Subsurface Microbiota – Choice of Carbon Source for Microcosm Enrichment and Isolation of Groundwater Bacteria – Xiaoqin Wu – bioRxiv

Genetic Evidence for Two Carbon Fixation Pathways (the Calvin-Benson-Bassham Cycle and the Reverse Tricarboxylic Acid Cycle) in Symbiotic and Free-Living Bacteria – Maxim Rubin-Blum – mSphere

Techniques
Generation of 13C-labeled MUC5AC mucin oligosaccharides for stable isotope probing of host-associated microbial communities – Clayton Evert – ACS Infectious Diseases

Transomics data-driven, ensemble kinetic modeling for system-level understanding and engineering of the cyanobacteria central metabolism – Hiroki Nishiguchi – Metabolic Engineering

Built environment/Microbes in Space
Pangenomic Approach To Understanding Microbial Adaptations within a Model Built Environment, the International Space Station, Relative to Human Hosts and Soil – Ryan A. Blaustein – mSystems
(Covered in the popular press as Good news: space bacteria (probably) aren’t evolving to destroy us)

Science, publishing, and career
Preprint: Tracking the popularity and outcomes of all bioRxiv preprints – Richard J. Abdill – bioRxiv

January 4, 2019

Highlights of today’s Digest include: animal microbiomes from snakes to bald eagles to porcupines, studies of bacteria promoting plant growth, and a nice review of ‘omics in fermented foods. Happy reading!

Human oral microbiome
Microcosm biofilms cultured from different oral niches in periodontitis patients – Fabian Cieplik – Journal of Oral Microbiology

Xylitol and sorbitol effects on the microbiome of saliva and plaque – Reisha Rafeek – Journal of Oral Microbiology

Human vaginal microbiome
Vaginal microbiome variances in sample groups categorized by clinical criteria of bacterial vaginosis – Hui-Mei Chen – BMC Genomics

Human gut microbiome
Five years of fecal microbiota transplantation – an update of the Israeli experience – Sharon A Greenberg – World Journal of Gastroenterology

Review: Association between the intestinal microbiota and allergic sensitization, eczema, and asthma: A systematic review – Petra Zimmermann – Journal of Allergy and Clinical Immunology

Interplay between food and gut microbiota in health and disease – Niels Banhos Danneskiold-Samsøe – Food Research International

Gut microbiome changes in overweight male adults following bowel preparation – Hui-Mei Chen – BMC Genomics

Animal Microbiome
Preprint: Bacterial Diversity in Feces of Wild Bald Eagles, Turkey Vultures and Common Ravens from the Pacific Northwest Coast, U.S.A. – Rocio Crespo – bioRxiv

Next-generation sequencing analysis reveals high bacterial diversity in wild venomous and non-venomous snakes from India – Sajesh Puthenpurackal Krishnankutty – Journal of Venomous Animals and Toxins including Tropical Diseases

Understanding the roles of surface proteins in regulation of Lactobacillus pentosus HC-2 to immune response and bacterial diversity in midgut of Litopenaeus vannamei – Yang Du – Fish & Shellfish Immunology

Characterization of novel lignocellulose-degrading enzymes from the porcupine microbiome using synthetic metagenomics – Mackenzie Thornbury – PLOS One

Plant, root, and soil microbiome
Review: Planting the Microbiome – Jennifer K. Spinler – Trends in Microbiology

Arabidopsis thaliana responds to colonisation of Piriformospora indica by secretion of symbiosis-specific proteins – Johannes Thürich – PLOS One

Screening of plant growth promotion ability among bacteria isolated from field-grown sorghum under different managements in Brazilian drylands – Jéssica Fernanda da Silva – World Journal of Microbiology and Biotechnology

Streptomyces: implications and interactions in plant growth promotion – Oluwaseyi Samuel Olanrewaju – Applied Microbiology and Biotechnology

Mycorrhizal features and leaf traits covary at the community level during primary succession – J. Rasmus P. Jespersen – Fungal Ecology

Microbial communities controlling methane and nutrient cycling in leach field soils – Cristina P.Fernandez-Baca – Water Research

Gradients of three coastal environments off the South China Sea and their impacts on the dynamics of heterotrophic microbial communities – Xianhua Liu – Science of the Total Environment

New insights into the impact of nZVI on soil microbial biodiversity and functionality – Carmen Fajardo – Journal of Environmental Science and Health, Part A

Syntrophic effect of indigenous and inoculated microorganisms in the leaching of rare earth elements from Western Australian monazite – Melissa K.Corbett – Research in Microbiology

Removal of veterinary antibiotics in constructed wetland microcosms – Response of bacterial communities – Filipa Santos – Ecotoxicology and Environmental Safety

Water and extremophile microbiome
Bacterial diversity in the water column of meromictic Lake Cadagno and evidence for seasonal dynamics – Francesco Danza – PLOS One

Microbial community succession and pollutants removal of a novel carriers enhanced duckweed treatment system for rural wastewater in Dianchi Lake basin – Guoke Chen – Bioresource Technology

Food Microbiology
Omics in traditional vegetable fermented foods and beverages – Jocelin Rizo – Critical Reviews in Food Science and Nutrition

Preprint: Construction of synthetic microbiota for reproducible flavor metabolism in Chinese light aroma type liquor produced by solid-state fermentation – Qun Wu – bioRxiv

Bioinformatics
A latent allocation model for the analysis of microbial composition and disease – Ko Abe – BMC Bioinformatics

Techniques
Metatranscriptomic and thermodynamic insights into medium-chain fatty acid production using an anaerobic microbiome – Matthew J. Scarborough – mSystems