Tag Archives: bioinformatics

March 27, 2023

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Human and General Microbiome

The genomic landscape of reference genomes of cultivated human gut bacteria – Xiaoqian Lin – Nature Communications

Inhibition of a Microbiota-derived Peptide Ameliorates Established Acute Lung Injury – Valeria Fridman D’Alessandro – The American Journal of Pathology

Eubiotic effect of rifaximin is associated with decreasing abdominal pain in symptomatic uncomplicated diverticular disease: results from an observational cohort study – Vladimir Ivashkin – BMC Gastroenterology

Mucin glycans drive oral microbial community composition and function – Chloe M Wu – NPJ Biofilms and Microbiomes

Changes in gut microbial community upon chronic kidney disease – Wu Liu – PloS One

A Pilot Study Exploring Temporal Development of Gut Microbiome/Metabolome in Breastfed Neonates during the First Week of Life – Imad Awan – Pediatric Gastroenterology, Hepatology & Nutrition

Realising respiratory microbiomic meta-analyses: time for a standardised framework – David Broderick – Microbiome

Vulvovaginal yeast infections during pregnancy and perinatal outcomes: systematic review and meta-analysis – Ranjana M S Gigi – BMC Women’s Health

Preprint: Hadza Prevotella Require Diet-derived Microbiota Accessible Carbohydrates to Persist in Mice – Rebecca H Gellman – bioRxiv

Review: Membrane lipids from gut microbiome-associated bacteria as structural and signalling molecules – Eileen Ryan – Microbiology

Review: Impact of Intermittent Fasting on the Gut Microbiota: A Systematic Review – Theodoro Pérez-Gerdel – Advanced Biology

Animal Microbiome

Wolbachia endosymbiotic bacteria alter the gut microbiome in the fly Drosophila nigrosparsa – Matsapume Detcharoen – Journal of Invertebrate Pathology

A symbiotic physical niche in Drosophila melanogaster regulates stable association of a multi-species gut microbiota – Ren Dodge – Nature Communications

Plant Microbiome

The core metabolome and root exudation dynamics of three phylogenetically distinct plant species – Sarah McLaughlin – Nature Communications

Co-occurrence network analysis unveils the actual differential impact on the olive root microbiota by two Verticillium wilt biocontrol rhizobacteria – Martina Cardoni – Environmental Microbiome

Environmental Microbiome

Investigating the eco-evolutionary response of microbiomes to environmental change – Jennifer B H Martiny – Ecology Letters

Microbiome Analysis: Resources, Tools and Techniques

In silico evaluation and selection of the best 16S rRNA gene primers for use in next-generation sequencing to detect oral bacteria and archaea – Alba Regueira-Iglesias – Microbiome

DeepGeni: deep generalized interpretable autoencoder elucidates gut microbiota for better cancer immunotherapy – Min Oh – Scientific Reports

Flex Meta-Storms elucidates the microbiome local beta-diversity under specific phenotypes – Mingqian Zhang – Bioinformatics

Preprint: Microbiome Preterm Birth DREAM Challenge: Crowdsourcing Machine Learning Approaches to Advance Preterm Birth Research – Jonathan L Golob – medRxiv

March 20, 2023

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Human and General Microbiome

Bacteria require phase separation for fitness in the mammalian gut – Emilia Krypotou – Science

Is there a placental microbiota? A critical review and re-analysis of published placental microbiota datasets – Jonathan J Panzer – BMC Microbiology

Gut-microbiome-expressed 3β-hydroxysteroid dehydrogenase degrades estradiol and is linked to depression in premenopausal females – Di Li – Cell Metabolism

Metagenomic association analysis of cognitive impairment in community-dwelling older adults – Jincheng Li – Neurobiology of Disease

Fusobacterium nucleatum promotes esophageal cancer early occurrence through upregulation of IL-32/PRTN3 expression – Jing Lei – Cancer Science

Review: Postbiotics Implication in the Microbiota-Host Intestinal Epithelial Cells Mutualism – Harpreet Kaur – Probiotics and Antimicrobial Proteins

Review: Microbiota and growth among infants and children in low-income and middle-income settings – James M Njunge – Current Opinion in Clinical Nutrition and Metabolic Care

Review: Cardiometabolic health, diet and the gut microbiome: a meta-omics perspective – Mireia Valles-Colomer – Nature Medicine

Review: Oral polymicrobial communities: Assembly, function, and impact on diseases – George Hajishengallis – Cell Host & Microbe

Review: Gut microbiota: a non-target victim of pesticide-induced toxicity – Tusha Sharma – Gut Microbes

Perspective: Human microbiome research: Growing pains and future promises – Jens Puschhof – PLoS Biology

Beneficial Microbes and Compounds

Versatility of bacterial outer membrane vesicles in regulating intestinal homeostasis – Xinyue Wang – Science Advances

Lactobacillus rhamnosus GG cell-free supernatant as a novel anti-cancer adjuvant – Rossella Salemi – Journal of Translational Medicine

Environmental Microbiome

Community dynamics of microbial eukaryotes in intertidal mudflats in the hypertidal Bay of Fundy – Eke I Kalu – ISME Communications

Other Microbes

Biointerface mineralization generates ultraresistant gut microbes as oral biotherapeutics – Zhongmin Geng – Science Advances

Genomic diversity of non-diarrheagenic fecal Escherichia coli from children in sub-Saharan Africa and south Asia and their relatedness to diarrheagenic E. coli – Tracy H Hazen – Nature Communications

Microbiome Analysis: Tools and Techniques

Spatial profiling of microbial communities by sequential FISH with error-robust encoding – Zhaohui Cao – Nature Communications

sBGC-hm: An atlas of secondary metabolite biosynthetic gene clusters from the human gut microbiome – Huixi Zou – Bioinformatics

Protocol: Bioinformatic and Statistical Analysis of Microbiome Data – Youngchul Kim – Methods in Molecular Biology

Protocol: Multi-omics Data Deconvolution and Integration: New Methods, Insights, and Translational Implications – Xuefeng Wang – Methods in Molecular Biology

March 6, 2023

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Human and General Microbiome

Assessment of microbiota in the gut and upper respiratory tract associated with SARS-CoV-2 infection – Jiarui Li – Microbiome

Population-level impacts of antibiotic usage on the human gut microbiome – Kihyun Lee – Nature Communications

A bacterial sulfoglycosidase highlights mucin O-glycan breakdown in the gut ecosystem – Toshihiko Katoh – Nature Chemical Biology

Microbiota-derived genotoxin tilimycin generates colonic stem cell mutations – Lisa Pöltl – Cell Reports

Review: Impact of caloric restriction on the gut microbiota – Lara Kern – Current Opinion in Microbiology

Animal Microbiome

Romboutsia lituseburensis JCM1404 supplementation ameliorated endothelial function via gut microbiota modulation and lipid metabolisms alterations in obese rats – Honggang Yin – FEMS Microbiology Letters

Disparate population and holobiont structure of pocilloporid corals across the Red Sea gradient demonstrate species-specific evolutionary trajectories – Carol Buitrago-López – Molecular Ecology

Omics and imaging combinatorial approach reveals butyrate-induced inflammatory effects in the zebrafish gut – Adrià López Nadal – Animal Microbiome

Gut microbiome is linked to functions of peripheral immune cells in transition cows during excessive lipolysis – Fengfei Gu – Microbiome

Maternal effects drive intestinal development beginning in the embryonic period on the basis of maternal immune and microbial transfer in chickens – Haizhou Gong – Microbiome

Mouse mammary tumor virus is implicated in severity of colitis and dysbiosis in the IL-10(-/-) mouse model of inflammatory bowel disease – Heather Armstrong – Microbiome

Microplastics affect arsenic bioavailability by altering gut microbiota and metabolites in a mouse model – Shan Chen – Environmental Pollution 

Substantial viral and bacterial diversity at the bat-tick interface – Ayda Susana Ortiz-Baez – Microbial Genomics

Review: Perturbation of maternal gut microbiota in mice during a critical perinatal window influences early neurobehavioral outcomes in offspring – Cassandre Morel – Neuropharmacology

Plant and Soil Microbiome

Local environment drives rapid shifts in composition and phylogenetic clustering of seagrass microbiomes – Melissa R Kardish – Scientific Reports

Experimental community coalescence sheds light on microbial interactions in soil and restores impaired functions – Sarah Huet – Microbiome

Microbiome Analysis: Tools and Techniques

Infants’ gut microbiome data: A Bayesian Marginal Zero-inflated Negative Binomial regression model for multivariate analyses of count data – Morteza Hajihosseini – Computational and Structural Biotechnology Journal

From defaults to databases: parameter and database choice dramatically impact the performance of metagenomic taxonomic classification tools – Robyn J Wright – Microbial Genomics

Using strain-resolved analysis to identify contamination in metagenomics data – Yue Clare Lou – Microbiome

Preprint: Transkingdom Network Analysis (TkNA): a systems approach inferring causal factors underlying host-microbiota interactions – Nolan K Newman – bioRxiv

February 27, 2023

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Highlights!

Extending and improving metagenomic taxonomic profiling with uncharacterized species using MetaPhlAn 4 – Aitor Blanco-Míguez – Nature Biotechnology

Gut microbial metabolism of 5-ASA diminishes its clinical efficacy in inflammatory bowel disease – Raaj S Mehta – Nature Medicine

Human and General Microbiome

Interpersonal variability of the human gut virome confounds disease signal detection in IBD – Stephen R Stockdale – Communications Biology

Clinical characteristics, diagnosis, outcomes and lung microbiome analysis of invasive pulmonary aspergillosis in the community-acquired pneumonia patients – Zhi Ao – BMJ Open Respiratory Research

Comparing the gut microbiome of obese, African American, older adults with and without mild cognitive impairment – Andrew McLeod – PloS One

Beneficial Microbes and Compounds

Capacity of a Microbial Synbiotic To Rescue the In Vitro Metabolic Activity of the Gut Microbiome following Perturbation with Alcohol or Antibiotics – Braden T Tierney – Applied and Environmental Microbiology

Animal Microbiome

A microbiota and dietary metabolite integrates DNA repair and cell death to regulate embryo viability and aneuploidy during aging – Robert Sonowal – Science Advances

A longitudinal survey in the wild reveals major shifts in fish host microbiota after parasite infection – Eglantine Mathieu-Bégné – Molecular Ecology

Matrine alleviates depressive-like behaviors via modulating microbiota-gut-brain axis in CUMS-induced mice – Ming Zhang – Journal of Translational Medicine

Variations in gut microbiome and metabolites of dogs with acute diarrhea in poodles and Labrador retrievers – Huasong Bai – Archives of Microbiology

Environmental Microbiome

Enzyme adaptation to habitat thermal legacy shapes the thermal plasticity of marine microbiomes – Ramona Marasco – Nature Communications

Microbiome Analysis: Tools and Techniques

Review: Computational methods and challenges in analyzing intratumoral microbiome data – Qi Wang – Trends in Microbiology

Robust Bioinformatics Approaches Result in the First Polygenic Risk Score for BMI in Greek Adults – Maria Kafyra – Journal of Personalized Medicine

Development of a tongue image-based machine learning tool for the diagnosis of gastric cancer: a prospective multicentre clinical cohort study – Li Yuan – EClinicalMedicine

Latent dirichlet allocation for double clustering (LDA-DC): discovering patients phenotypes and cell populations within a single Bayesian framework – Elie-Julien El Hachem – BMC Bioinformatics

February 24, 2023

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Human and General Microbiome

Review: Gut microbiome lipid metabolism and its impact on host physiology – Brown et al. Cell Host & Microbe

Review: Modelling human immune responses using microbial exposures in rodents – Li and Baldridge. Nature Microbiology

Gut commensal Parabacteroides distasonis alleviates inflammatory arthritis – Sun et al. Gut

An open label, non-randomized study assessing a prebiotic fiber intervention in a small cohort of Parkinson’s disease participants – Hall et al. Nature Communications

Antibiotic use and inflammatory bowel disease: number needed to harm? – Ludvigsson. Gut

Oral & Respiratory Microbiome

Oral mucosal breaks trigger anti-citrullinated bacterial and human protein antibody responses in rheumatoid arthritis – Brewer et al. Science Translational Medicine

Sputum bacterial load and bacterial composition correlate with lung function and are altered by long-term azithromycin treatment in children with HIV-associated chronic lung disease – Abotsi et al. Microbiome

Animal experiments

Genetic mapping of microbial and host traits reveals production of immunomodulatory lipids by Akkermansia muciniphila in the murine gut – Zhang et al. Nature Microbiology

Microbe-mediated intestinal NOD2 stimulation improves linear growth of undernourished infant mice – Schwarzer et al. Science

Gamma-delta T cells modulate the microbiota and fecal micro-RNAs to maintain mucosal tolerance – Rezende et al. Microbiome

Phages and viruses

Review: Bacteriophage discovery to advance biotechnology and biotherapeutics – Mu and Lawley Nature Reviews Microbiology

Bioinformatics

Impact of microbial genome completeness on metagenomic functional inference – Eisenhofer et al. ISME

Pharokka: a fast scalable bacteriophage annotation tool – Bouras et al. Bioinformatics

Non Microbiome Picks

A systems immunology study comparing innate and adaptive immune responses in adults to COVID-19 mRNA and adenovirus vectored vaccines – Ryan et al. Cell Reports Medicine

Influenza-trained mucosal-resident alveolar macrophages confer long-term antitumor immunity in the lungs – Wang et al. Nature Immunology

February 20, 2023

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Human and General Microbiome

Review: Controlling the human microbiome – Yang-Yu Liu – Cell Systems

Review: Metabolic models of human gut microbiota: Advances and challenges – Daniel Rios Garza – Cell Systems

The fecal microbiotas of women of Pacific and New Zealand European ethnicities are characterized by distinctive enterotypes that reflect dietary intakes and fecal water content – Nikki Renall – Gut Microbes

Identifying the Novel Gut Microbial Metabolite Contributing to Metabolic Syndrome in Children Based on Integrative Analyses of Microbiome-Metabolome Signatures – Jia Wei – Microbiology Spectrum

Gut Microbiome and Risk of Ischemic Stroke: A Comprehensive Mendelian Randomization Study – Changjiang Meng – European Journal of Preventive Cardiology

Ancient Microbiome

Metagenomic analysis of Ancient Egyptian canopic jars – Enrique Rayo – American Journal of Biological Anthropology

Animal Model Microbiome

Preprint: Vaginal microbial dynamics and pathogen colonization in a humanized microbiota mouse model – Marlyd E Mejia – bioRxiv

Plant Microbiome

Multidisciplinary evaluation of plant growth promoting rhizobacteria on soil microbiome and strawberry quality – Jun Haeng Nam – AMB Express

Environmental Microbiome

Unravelling microalgal-bacterial interactions in aquatic ecosystems through 16S rRNA gene-based co-occurrence networks – B L D Uthpala Pushpakumara – Scientific Reports

Microbiome Analysis and Techniques

gutSMASH predicts specialized primary metabolic pathways from the human gut microbiota – Victòria Pascal Andreu – Nature Biotechnology

Reliability of species detection in 16S microbiome analysis: Comparison of five widely used pipelines and recommendations for a more standardized approach – Andreas Hiergeist – PloS One

Preprint: Impact of experimental bias on compositional analysis of microbiome data – Yingtian Hu – bioRxiv

January 27, 2023

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General Microbiome

Questioning the fetal microbiome illustrates pitfalls of low-biomass microbial studies – Kennedy et al. Nature

Microbial foods for improving human and planetary health – Jahn et al. Cell

A tissue atlas of ulcerative colitis revealing evidence of sex-dependent differences in disease-driving inflammatory cell types and resistance to TNF inhibitor therapy – Mayer et al. Science Advances

Associations of the skin, oral and gut microbiome with aging, frailty and infection risk reservoirs in older adults – Larson et al. Nature Aging

Bacteriophage / Virome

Phage therapy: From biological mechanisms to future directions – Strathdee et al. Cell

Mining metatranscriptomes reveals a vast world of viroid-like circular RNAs – Lee et al. Cell

Water and extremophile microbiome

High-resolution metagenomic reconstruction of the freshwater spring bloom – Kavagutti et al. Microbiome

Closed genomes uncover a saltwater species of Candidatus Electronema and shed new light on the boundary between marine and freshwater cable bacteria – Sereika et al. ISME

Bioinformatics

Enhanced correlation-based linking of biosynthetic gene clusters to their metabolic products through chemical class matching – Louwen et al. Microbiome

PLSDA-batch: a multivariate framework to correct for batch effects in microbiome data – Wang & Cao. Briefings in Bioinformatics

Genome-scale metabolic reconstruction of 7,302 human microorganisms for personalized medicine – Heinken et al. Nature Biotechnology

Non-Microbiome picks

Infection infidelities drive innate immunity – Kagan. Science

Functional T cells are capable of supernumerary cell division and longevity – Soerens et al. Nature

Genetic adaptation to pathogens and increased risk of inflammatory disorders in post-Neolithic Europe – Kerner et al. Cell Genomics

December 19, 2022

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Highlights!

Multi-omic interactions in the gut of children at the onset of islet autoimmunity – Patrick G Gavin – Microbiome

“Here, we apply an integrative approach to combine comprehensive fecal virome, microbiome, and metaproteome data sampled before and at the onset of islet autoimmunity in 40 children at increased risk of T1D […] We show a functional remodeling of the gut microbiota accompanies both islet autoimmunity and viral infection with a switch in function in Faecalibacterium occurring at the onset of islet autoimmunity.”

Human and General Microbiome

Review: The microbiota-gut-brain axis in pathogenesis of depression: a narrative review – Hui Yao – Physiology & Behavior

Review: Environmental enteric dysfunction: gut and microbiota adaptation in pregnancy and infancy – Carrie A Cowardin – Nature Reviews. Gastroenterology & Hepatology

Review: Gastrointestinal Tract, Microbiota and Multiple Sclerosis (MS) and the Link Between Gut Microbiota and CNS – Bahman Yousefi – Current Microbiology

Effect of proton pump inhibitors in infants with esophageal atresia on the gut microbiome: a pilot cohort – Nele Brusselaers – Gut Pathogens

Endodontic microbial communities in apical periodontitis – Alessio Buonavoglia – Journal of Endodontics

Gut Microbiota-Generated Phenylacetylglutamine and Heart Failure – Kymberleigh A Romano – Circulation. Heart Failure

Animal Microbiome

Midgut Bacterial Microbiota of 12 Fish Species from a Marine Protected Area in the Aegean Sea (Greece) – Konstantinos Kormas – Microbial Ecology

Guts within guts: the microbiome of the intestinal helminth parasite Ascaris suum is derived but distinct from its host – Ankur Midha – Microbiome

Plant Microbiome

Multifaceted roles of flavonoids mediating plant-microbe interactions – Lanxiang Wang – Microbiome

Microbiome Analysis and Techniques

An economic and robust TMT labeling approach for high throughput proteomic and metaproteomic analysis – Marybeth Creskey – Proteomics

Machine learning-derived gut microbiome signature predicts fatty liver disease in the presence of insulin resistance – Baeki E Kang – Scientific Reports

Pseudomonas-specific 16S rRNA insect gut-microbiome profiling using next-generation sequencing – Ayushi Gupta – STAR Protocols

December 2, 2022

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Human and General Microbiome

Different Characteristics in Gut Microbiome between Advanced Adenoma Patients and Colorectal Cancer Patients by Metagenomic Analysis – Shuwen Han – Microbiology Spectrum

The Spatial Features and Temporal Changes in the Gut Microbiota of a Healthy Chinese Population – Wen Zhang – Microbiology Spectrum

The Gut Microbiota is Important for the Maintenance of Blood-Cerebrospinal Fluid Barrier Integrity – Emily G Knox – The European Journal of Neuroscience

Evaluation of co-circulating pathogens and microbiome from COVID-19 infections – James B Thissen – PloS One

A Clinical Study Provides the First Direct Evidence That Interindividual Variations in Fecal β-Lactamase Activity Affect the Gut Mycobiota Dynamics in Response to β-Lactam Antibiotics – Margot Delavy – mBio

Clostridia isolated from helminth-colonized humans promote the life cycle of Trichuris species – Shushan Sargsian – Cell Reports

Genome Watch: Zooming into the structure of the microbiome – Gemma G R Murray – Nature Reviews. Microbiology

Beneficial Microbes and Compounds

Saussurea involucrata oral liquid regulates gut microbiota and serum metabolism during alleviation of collagen-induced arthritis in rats – Shan Cong – Phytotherapy Research

Prebiotic oligofructose protects against high-fat diet-induced obesity by changing the gut microbiota, intestinal mucus production, glycosylation and secretion – Paola Paone – Gut Microbes

Review: Predicting Personalized Responses to Dietary Fiber Interventions: Opportunities for Modulation of the Gut Microbiome to Improve Health – Car Reen Kok – Annual Review of Food Science and Technology

Animal Microbiome

Gut dysbiosis induces the development of mastitis through a reduction in host anti-inflammatory enzyme activity by endotoxemia – Caijun Zhao – Microbiome

Chronic clinical signs of upper respiratory tract disease associate with gut and respiratory microbiomes in a cohort of domestic felines – Holly Kristin Arnold – PloS One

Plant and Soil Microbiome

Bio-Organic Fertilizer Promotes Pear Yield by Shaping the Rhizosphere Microbiome Composition and Functions – Zhonghua Wang – Microbiology Spectrum

Impacts of maize hybrids with different nitrogen use efficiency on root-associated microbiota based on distinct rhizosphere soil metabolites – Keke Li – Environmental Microbiology

Environmental Microbiome

Coupled C, H, N, S and Fe biogeochemical cycles operating in the continental deep subsurface of the Iberian Pyrite Belt – Ricardo Amils – Environmental Microbiology

Long-Read Sequencing Improves Recovery of Picoeukaryotic Genomes and Zooplankton Marker Genes from Marine Metagenomes – N V Patin – mSystems

Bioinformatics and Microbiome Analysis

The Application of Spearman Partial Correlation for Screening Predictors of Weight Loss in a Multiomics Dataset – Joel Correa da Rosa – Omics

Sampling of Human Microbiomes to Screen for Antibiotic-Producing Commensals – Benjamin Torres Salazar – Methods in Molecular Biology

November 26, 2022

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Human and General Microbiome

Essay: Autobiography of a gut bacterium – Florian Schmidt – Science

Untargeted Fecal Metabolomic Analyses across an Industrialization Gradient Reveal Shared Metabolites and Impact of Industrialization on Fecal Microbiome-Metabolome Interactions – Jacob J Haffner – mSystems

Diet standardization reduces intra-individual microbiome variation – Clara Delaroque – Gut Microbes

Investigation of the gut microbiome, bile acid composition and host immunoinflammatory response in a model of azoxymethane-induced colon cancer at discrete timepoints – J M Keane – British Journal of Cancer

A comparative study to determine the association of gut microbiome with schizophrenia in Zhejiang, China – Fuyang Yan – BMC Psychiatry

Review: Gut Microbiome Analysis for Personalized Nutrition: The State of Science – Marie-Christine Simon – Molecular Nutrition & Food Research

Review: The nonindustrialised microbiome in a modern world – Fergus Shanahan – Clinical Science

Beneficial Microbes and Compounds

A gut microbial metabolite of dietary polyphenols reverses obesity-driven hepatic steatosis – Lucas J Osborn – PNAS

Akkermansia muciniphila ameliorates depressive disorders in a murine alcohol-LPS (mALPS) model – Dingming Guo – Food & Function

Animal Microbiome

The Kitty Microbiome Project: Defining the Healthy Fecal Core Microbiome in Pet Domestic Cats – Holly H Ganz – Veterinary Sciences

Bioinformatics and Microbiome Analysis

Bioinformatic Approaches for Describing the Oral Microbiota – Kristi Biswas – Methods in Molecular Biology

Predicting butyrate- and propionate-forming bacteria of gut microbiota from sequencing data – Berenike Kircher – Gut Microbes

Review: Machine learning for data integration in human gut microbiome – Peishun Li – Microbial Cell Factories

More Microbes 

Impact of innovative nanoadditives on biodigesters microbiome – Fatma Y Hassaneen – Microbial Biotechnology

Microbiome analysis in Lascaux Cave in relation to black stain alterations of rock surfaces and collembola – Lise Alonso – Environmental Microbiology Reports