Category Archives: General Microbiome

October 12, 2022

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General microbiome

Global airborne bacterial community—interactions with Earth’s microbiomes and anthropogenic activities – Zhao et al. – PNAS

Tumor microbiome links cellular programs and immunity in pancreatic cancer – Cancer Cell – Ghaddar et al. – Cancer Cell

Human wound microbiome

The Wound Microbiome – White & Grice – Cold Spring Harbor Perspectives in Biology

Human gut microbiome

Pivotal interplays between fecal metabolome and gut microbiome reveal functional signatures in cerebral ischemic stroke – Zhou et al. – Journal of Translational Medicine volume

Gut-Testis Axis: Microbiota Prime Metabolome To Increase Sperm Quality in Young Type 2 Diabetes – Yan et al. – Microbiology Spectrum

Multi-angle meta-analysis of the gut microbiome in Autism Spectrum Disorder: a step toward understanding patient subgroups – West et al. – Scientific Reports

[REVIEW]The role of the gut microbiota in health and cardiovascular diseases – Wang et al. – Molecular Biomedicine

Animal microbiome

Airborne polystyrene microplastics and nanoplastics induce nasal and lung microbial dysbiosis in mice – Zha et al. – Chemosphere

Effects of urban particulate matter on gut microbiome and partial schizophrenia-like symptoms in mice: Evidence from shotgun metagenomic and metabolomic profiling – Yi et al. – Science of The Total Environment

Lactococcus lactis’ Effect on the Intestinal Microbiota of Streptococcus agalactiae-Infected Zebrafish (Danio rerio) – Tan et al. – Microbiology Spectrum

Exploring AI-2-mediated interspecies communications within rumen microbial communities – Liu et al. – Microbiome

Microbiome-driven breeding strategy potentially improves beef fatty acid profile benefiting human health and reduces methane emissions – Martinez-Alvaro et al. – Microbiome

Chicken intestinal microbiota modulation of resistance to nephropathogenic infectious bronchitis virus infection through IFN-I – Yin et al. – Microbiome

Plant, root, and soil microbiome

[CORRESONDENCE]Functionally-explicit sampling can answer key questions about the specificity of plant–microbe interactions – Fleishman et al. – Environmental Microbiome

Dissecting the cotranscriptome landscape of plants and their microbiota – Nobori et al. – EMBO Reports

Bioinformatics

MiMeDB: the Human Microbial Metabolome Database – Wishart et al. – NAR

gutMDisorder v2.0: a comprehensive database for dysbiosis of gut microbiota in phenotypes and interventions – Qi et al. – NAR

October 10, 2022

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Human and General Microbiome

The hallmarks of dietary intervention-resilient gut microbiome – Natalia S Klimenko – NPJ Biofilms and Microbiomes

Nutrition and Microbiome Interactions in Human Cancer – Phillip J Daschner – Journal of the Academy of Nutrition and Dietetics

Differences in the microbiota of oral rinse, lesion, and normal site samples from patients with mucosal abnormalities on the tongue – Yawaka Shitozawa – Scientific Reports

Dynamic changes in host immune system and gut microbiota are associated with the production of SARS-CoV-2 antibodies – Maozhen Han – Gut

Antibiotics and probiotics impact gut antimicrobial resistance gene reservoir in COVID-19 patients – Qi Su – Gut Microbes

Fibre is good for the microbiome: but what is the evidence? – Kevin Whelan – The Lancet. Gastroenterology & Hepatology

Model Animal Microbiome

Enhanced cultured diversity of the mouse gut microbiota enables custom-made synthetic communities – Afrizal Afrizal – Cell Host & Microbe

Non-Model Animal Microbiome

Convergent evolution of the gut microbiome in marine carnivores – Xibao Wang – Ecology and Evolution

Gut microbiota shift in layer pullets fed on black soldier fly larvae-based feeds towards enhancing healthy gut microbial community – Evalyne W Ndotono – Scientific Reports

Succession of the intestinal bacterial community in Pacific bluefin tuna (Thunnus orientalis) larvae – Akito Taniguchi – PloS One

Plant Microbiome

Bacterial community in soil and tree roots of Picea abies shows little response to clearcutting – Tijana Martinović – FEMS Microbiology Ecology

Environmental Microbiome

Size-fractionated microbiome observed during an eight-month long sampling in Jiaozhou Bay and the Yellow Sea – Jianchang Tao – Scientific Data

Food Microbiome

Microbiome of rehydrated corn and sorghum grain silages treated with microbial inoculants in different fermentation periods – Mariele Cristina Nascimento Agarussi – Scientific Reports

Microbiome Analysis

Quantification and characterization of mouse and human tissue-resident microbiota by qPCR and 16S sequencing – Bingqing Yao – STAR Protocols

October 3, 2022

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Human and General Microbiome

Mucus-degrading Bacteroides link carbapenems to aggravated graft-versus-host disease – Eiko Hayase – Cell

Pan-cancer analyses reveal cancer-type-specific fungal ecologies and bacteriome interactions – Lian Narunsky-Haziza – Cell

A pan-cancer mycobiome analysis reveals fungal involvement in gastrointestinal and lung tumors – Anders B Dohlman – Cell

Gut microbiota of hepatitis B virus-infected patients in the immune-tolerant and immune-active phases and their implications in metabolite changes – Ya-Nan Li – World Journal of Gastroenterology

Streptococcus mutans promotes tumor progression in oral squamous cell carcinoma – Ming-Shao Tsai – Journal of Cancer

Short-chain fatty acid concentrations in the incidence and risk-stratification of colorectal cancer: a systematic review and meta-analysis – Ehsan Alvandi – BMC Medicine

Mycobacterium potentiates protection from colorectal cancer by gut microbial alterations – Yu-Mi Kim – Immunology

Nutrition, Immunosenescence, and Infectious Disease: An Overview of the Scientific Evidence on Micronutrients and on Modulation of the Gut Microbiota – Philip C Calder – Advances in Nutrition 

Unfermented β-fructan fibers fuel inflammation in select inflammatory bowel disease patients – Heather K Armstrong – Gastroenterology

Machine-learning algorithms for asthma, COPD, and lung cancer risk assessment using circulating microbial extracellular vesicle data and their application to assess dietary effects – Andrea McDowell – Experimental & Molecular Medicine

Microbiome ethics, guiding principles for microbiome research, use and knowledge management – Lene Lange – Environmental Microbiome

Review: The gut mycobiome in health, disease, and clinical applications in association with the gut bacterial microbiome assembly – Fen Zhang – The Lancet. Microbe

Beneficial Microbes and Compounds

Review: Tailoring gut microbiota with a combination of Vitamin K and probiotics as a possible adjuvant in the treatment of rheumatic arthritis: a systematic review – Luciana Pereira – Clinical Nutrition ESPEN

Dietary Isoflavones Alter Gut Microbiota and Lipopolysaccharide Biosynthesis to Reduce Inflammation – Sudeep Ghimire – Gut Microbes

Bacteroides thetaiotaomicron rough-type lipopolysaccharide: The chemical structure and the immunological activity – Molly Dorothy Pither – Carbohydrate Polymers

Animal Microbiome

Study of cattle microbiota in different regions of Kazakhstan using 16S metabarcoding analysis – Aida Daugaliyeva – Scientific Reports

Microscopic marine invertebrates are reservoirs for cryptic and diverse protists and fungi – Corey C Holt – Microbiome

Plant Microbiome

Review: Microbiomes in agroecosystem: Diversity, function and assembly mechanisms – Chao Xiong – Environmental Microbiology Reports

Bioinformatics and Microbiome Analysis

Integrating Phylogenetic and Functional Data in Microbiome Studies – Gavin M Douglas – Bioinformatics 

Higher off-target amplicon detection rate in MiSeq v3 compared to v2 reagent kits in the context of 16S-rRNA-sequencing – Mari-Lee Odendaal – Scientific Reports

September 28, 2022

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General microbiome

[Personal View]Causal discovery for the microbiome – Corander, Hanage & Pensar – The Lancet Microbe

Integrative functional analysis uncovers metabolic differences between Candida species – Begum et al. – Communications Biology

Human skin microbiome

Evolution of the facial skin microbiome during puberty in normal and acne skin – Schneider et al. – JEADV

Human gut microbiome

[REVIEW]Harnessing Microbiota to Improve Immunotherapy for Gastrointestinal Cancers – Goc & Sonnenberg – Cancer Immunol Res

[REVIEW]Gut microbiome in multiple sclerosis-related cognitive impairment – Ghadiri et al. – Multiple Sclerosis and Related Disorders

[REVIEW]The Microbiome in Gastrointestinal Cancers – White & Wargo – Gastroenterology Clinics of North America

Human gut microbiota and its metabolites impact immune responses in COVID-19 and its complications – Nagata et al. – Gastroenterology

Gut microbial fermentation promotes the intestinal anti-inflammatory activity of Chinese yam polysaccharides – Bai et al. – Food Chemistry

Animal experiments (mouse/rat experiments, chickens/pigs on different diets)

The preventive effects of probiotic Akkermansia muciniphila on D-galactose/AlCl3 mediated Alzheimer’s disease-like rats – He et al. – Experimental Gerontology

Characterizing the chicken gut colonization ability of a diverse group of bacteria – Poudel et al. – Poultry Science

Obesity induced gut dysbiosis contributes to disease severity in an animal model of multiple sclerosis – Shahi et al. – Front. Immunol.

Animal microbiome (for animals in the wild)

Impact of aluminum exposure on oxidative stress, intestinal changes and immune responses in red swamp crayfish (Procambarus clarkii) – Zhang et al. – Science of The Total Environment

Network analysis reveals significant joint effects of microplastics and tetracycline on the gut than the gill microbiome of marine medaka – Liao et al. – Journal of Hazardous Materials

Xenobiotic estradiol-17ß alters gut microbiota of hatchling American Alligators (Alligator mississippiensis) – Murphy et al. – Environmental Microbiology

Sustained Drought, but Not Short-Term Warming, Alters the Gut Microbiomes of Wild Anolis Lizards – Williams et al. – Applied and Environmental Microbiology

Water and extremophile microbiome (sea, rivers, lakes, glaciers, permafrost, high-salt)

Microbial Composition of Freshwater Marsh Sediment Responds more Strongly to Microcosm Seawater Addition than Simulated Nitrate or Phosphate Eutrophication – Weingarten & Jackson – Microbial Ecology

Built environment (subways, indoor surfaces)

Microbial community regulation and performance enhancement in gas biofilters by interrupting bacterial communication – Wang et al. – Microbiome

Bioinformatics

Identification of microbial features in multivariate regression under false discovery rate control – Srinivasan, Xue and Zhan – Computational Statistics & Data Analysis

Techniques

Strain-level resolution and pneumococcal carriage dynamics by single-molecule real-time (SMRT) sequencing of the plyNCR marker: a longitudinal study in Swiss infants – Oyewole et al. – Microbiome

September 24, 2022

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Human and General Microbiome

Systemic antibody responses against human microbiota flagellins are overrepresented in chronic fatigue syndrome patients – Thomas Vogl – Science Advances

Strain-level resolution and pneumococcal carriage dynamics by single-molecule real-time (SMRT) sequencing of the plyNCR marker: a longitudinal study in Swiss infants – Oluwaseun Rume-Abiola Oyewole – Microbiome

Longitudinal disease-associated gut microbiome differences in infants with food protein-induced allergic proctocolitis – Victoria M Martin – Microbiome

Host and gut bacteria share metabolic pathways for anti-cancer drug metabolism – Peter Spanogiannopoulos – Nature Microbiology

Diet-driven microbial ecology underpins associations between cancer immunotherapy outcomes and the gut microbiome – Rebecca C Simpson – Nature Medicine

Advances in the gut microbiome and mood disorders – Sabrina Mörkl – Current Opinion in Psychiatry

Review: Modulation of the intestinal microbiota impacts the efficacy of immunotherapy in cancer patients – A recent literature survey – Stella Ziegler – European Journal of Microbiology & Immunology

Animal Microbiome

Metagenomics-resolved genomics provides novel insights into chitin turnover, metabolic specialization, and niche partitioning in the octocoral microbiome – Tina Keller-Costa – Microbiome

Intestinal microbiome-mediated resistance against vibriosis for Cynoglossus semilaevis – Qian Zhou – Microbiome

Plant Microbiome

Response of soil microecology to different cropping practice under Bupleurum chinense cultivation – Li Liu – BMC Microbiology

Community Assembly of Fungi and Bacteria along Soil-Plant Continuum Differs in a Zoige Wetland – Jie Li – Microbiology Spectrum

Review: Investigating plant-microbe interactions within the root – Yuniar Devi Utami – Archives of Microbiology

Food Microbiome

Geographically Associated Fungus-Bacterium Interactions Contribute to the Formation of Geography-Dependent Flavor during High-Complexity Spontaneous Fermentation – Yuwei Tan – Microbiology Spectrum

More Microbes

A meta-analysis of acetogenic and methanogenic microbiomes in microbial electrosynthesis – Simon Mills – NPJ Biofilms and Microbiomes

Bioinformatics and Microbiome Analysis

MicrobiomeCensus estimates human population sizes from wastewater samples based on inter-individual variability in gut microbiomes – Lin Zhang – PLoS Computational Biology

September 22, 2022

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Happy almost Friday! Today’s digest includes a time series tracking changes after fecal transplant, biofilm-formation analysis from isolations from swine slaughterhouses as well as techniques to improve computational notebooks, rapid genotyping, and more.

Enjoy!

Human gut microbiome

Time series strain tracking analysis post fecal transplantation identifies individual specific patterns of fecal dominant donor, recipient, and unrelated microbial strains – Koo & Morrow – PLOS One

Animal experiments

Microbiome complexity shapes metabolism – Litichevskiy & Thaiss – PLOS Biology

Minimal overall divergence of the gut microbiome in an adaptive radiation of Cyprinodon pupfishes despite potential adaptive enrichment for scale-eating – Heras & Martin – PLOS One

Molecular characterization and biofilm-formation analysis of Listeria monocytogenes, Salmonella spp., and Escherichia coli isolated from Brazilian swine slaughterhouses – Santos et al. – PLOS One

Animal microbiome

Ecology and distribution of Leptospira spp., reservoir hosts and environmental interaction in Sri Lanka, with identification of a new strain – Sluydts et al. – PLOS Neglected Tropical Diseases

Techniques

A simple kit to use computational notebooks for more openness, reproducibility, and productivity in research – Figueiredo et al. – PLOS Computational Biology

Bacterial concentration and Campylobacter spp. quantification differ when fresh or ultra-frozen samples are analysed over time using molecular biology and culture-based methods – Khattak et al. – Plos One

Robust inference of population size histories from genomic sequencing data – Upadhya & Steinrücken – PLOS Computational Biology

Rapid genotyping of targeted viral samples using Illumina short-read sequencing data – Váradi et al. – PLOS One

Improved assessments of bulk milk microbiota composition via sample preparation and DNA extraction methods – Xue & Marco – PLOS ONE

September 18, 2022

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Human and General Microbiome

Neisseria species as pathobionts in bronchiectasis – Liang Li – Cell Host & Microbe

The gut microbiome molecular complex in human health and disease – Paul Wilmes – Cell Host & Microbe

Codiversification of gut microbiota with humans – Taichi A Suzuki – Science

Gut microbiome of multiple sclerosis patients and paired household healthy controls reveal associations with disease risk and course – The iMSMS Consortium – Cell

Composition and diverse differences of intestinal microbiota in ulcerative colitis patients – Siying Zhu – Frontiers in Cellular and Infection Microbiology

A systematic review on omics data (metagenomics, metatranscriptomics, and metabolomics) in the role of microbiome in gallbladder disease – Paola Di Carlo – Frontiers in Physiology

Variability of strain engraftment and predictability of microbiome composition after fecal microbiota transplantation across different diseases – Gianluca Ianiro – Nature Medicine

Drivers and determinants of strain dynamics following fecal microbiota transplantation – Thomas S B Schmidt – Nature Medicine

Long-term ecological and evolutionary dynamics in the gut microbiomes of carbapenemase-producing Enterobacteriaceae colonized subjects – Jonathan T L Kang – Nature Microbiology

Structural and functional dysbiosis of gut microbiota in Tibetan subjects with coronary heart disease – Qi Cheng – Genomics

Growth of succinate consumer Dialister hominis is supported by Bacteroides thetaiotaomicron – Mitsuo Sakamoto – Anaerobe

RhoB affects colitis through modulating cell signaling and intestinal microbiome – Jianming Yang – Microbiome

Review: Diet fuelling inflammatory bowel diseases: preclinical and clinical concepts – Timon E Adolph – Gut

Review: Recent findings in Akkermansia muciniphila-regulated metabolism and its role in intestinal diseases – Meng-Jie Liu – Clinical Nutrition

Beneficial Microbes and Compounds

Comprehensive analysis of microbiome, metabolome and transcriptome revealed the mechanisms of Moringa oleifera polysaccharide on preventing ulcerative colitis – Hanchen Tian – International Journal of Biological Macromolecules

Probiotics ameliorates pulmonary inflammation via modulating gut microbiota and rectifying Th17/Treg imbalance in a rat model of PM2.5 induced lung injury – Yongcan Wu – Ecotoxicology and Environmental Safety

Short-term supplementation with ω-3 polyunsaturated fatty acids modulates primarily mucolytic species from the gut luminal mucin niche in a human fermentation system – Charlène Roussel – Gut Microbes

Model Animal Microbiome

Interactive Effect of Combined Intermittent and Sustained Hypoxia and High-Fat Diet on the Colonic Mucosal Microbiome and Host Gene Expression in Mice – Saif Mashaqi – Nature and Science of Sleep

Non-Model Animal Microbiome

Fungi are more transient than bacteria in caterpillar gut microbiomes – Martin Šigut – Scientific Reports

Adapting to climate with limited genetic diversity: Nucleotide, DNA methylation and microbiome variation among populations of the social spider Stegodyphus dumicola – Anne Aagaard – Molecular Ecology

Bioinformatics and Microbiome Analysis

Filtering ASVs/OTUs via mutual information-based microbiome network analysis – Elham Bayat Mokhtari – BMC Bioinformatics

Batch effects removal for microbiome data via conditional quantile regression – Wodan Ling – Nature Communications

Phylogenetic Analysis of Anti-CRISPR and Member Addition in the Families – Sweta Nidhi – Molecular Biotechnology

Shallow shotgun sequencing of the microbiome recapitulates 16S amplicon results and provides functional insights – Mason R Stothart – Molecular Ecology Resources

SnapShot: The Expobiome Map – Velma T E Aho – Cell Host & Microbe

September 14, 2022

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General microbiome

[PREPRINT]Cross-biome microbial networks reveal functional redundancy and suggest genome reduction through functional complementarity – Puente-Sánchez et al. – bioRiv

Human airway microbiome

[PREPRINT]Genomic and ecologic characteristics of the airway microbial-mucosal complex – Cuthbertson et al. – bioRxiv

Animal microbiome (for animals in the wild)

[DATA ]A global dataset of microbial community in ticks from metagenome study – Liu et al. – Scientific Data

Highland adaptation of birds on the Qinghai-Tibet Plateau via gut microbiota – Liu et al. – Applied Microbiology and Biotechnology

Water and extremophile microbiome (sea, rivers, lakes, glaciers, permafrost, high-salt)

[PREPRINT][Microbial community dynamics during a harmful Chrysochromulina leadbeateri bloom in northern Norway](Microbial community dynamics during a harmful Chrysochromulina leadbeateri bloom in northern Norway) – Aalto et al. – bioRxiv

September 12, 2022

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Human and General Microbiome

CAR-T cell therapy-related cytokine release syndrome and therapeutic response is modulated by the gut microbiome in hematologic malignancies – Yongxian Hu – Nature Communications

Untangling the link between the human gut microbiota composition and the severity of the symptoms of the COVID-19 infection – Leonardo Mancabelli – Environmental Microbiology

Trimethylamine-N-oxide (TMAO) promotes balloon injury-induced neointimal hyperplasia via upregulating Beclin1 and impairing autophagic flux – Qingqing Hong – Biomedicine & Pharmacotherapy 

Weizmannia faecalis sp. nov., isolated from a human stool sample – Hoang Thong Kieu – Archives of Microbiology

Fusobacterium nucleatum aggravates ulcerative colitis through promoting gut microbiota dysbiosis and dysmetabolism – Shulan Lin – Journal of Periodontology

The evaluation of fecal microbiota transplantation vs vancomycin in a Clostridioides difficile infection model – Qiaomai Xu – Applied Microbiology and Biotechnology

Review: The early-life gut microbiome and vaccine efficacy – Anne Jordan – The Lancet. Microbe

Review: Crucial nuances in understanding (mis)associations between the neonatal microbiome and Cesarean delivery – Alexa M Sassin – Trends in Molecular Medicine

Beneficial Microbes and Compounds

L-Theanine regulates lipid metabolism by modulating gut microbiota and bile acid metabolism – Wei Xu – Journal of the Science of food and Agriculture

Structural and prebiotic activity analysis of the polysaccharide produced by Lactobacillus helveticus SNA12 – Xiaomeng Wang – Carbohydrate Polymers

Review: Unlocking a novel determinant of athletic performance: The role of the gut microbiota, short-chain fatty acids, and biotics in exercise – Kate M Sales – Journal of Sport and Health Science

Animal Microbiome

Comparative analysis of gut microbiota and immune genes linked with the immune system of wild and captive Spodoptera frugiperda (Lepidoptera: Noctuidae) – Renwen Zheng – Developmental and Comparative Immunology

A global dataset of microbial community in ticks from metagenome study – Mei-Chen Liu – Scientific Data

Exposure to dechlorane 602 induces perturbation of gut immunity and microbiota in female mice – Yunping Li – Environmental Pollution 

Plant Microbiome

Dynamics of bacterial and fungal communities of mango: From the tree to ready-to-Eat products – Ahmed Taïbi – Food Microbiology

Forensic Microbiome

The microbiome of fly organs and fly-human microbial transfer during decomposition – Heather L Deel – Forensic Science International

September 10, 2022

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Human and General Microbiome

Evolution of the Gut Microbiome in HIV-Exposed Uninfected and Unexposed Infants during the First Year of Life – Conner L Jackson – mBio

Gastrointestinal microbiota profile and clinical correlations in advanced EGFR-WT and EGFR-mutant non-small cell lung cancer – Woraseth Saifon – BMC Cancer

Hybrid metagenome assemblies link carbohydrate structure with function in the human gut microbiome – Anuradha Ravi – Communications Biology

Genetic Determinants of Hydrogen Sulfide Biosynthesis in Fusobacterium nucleatum Are Required for Bacterial Fitness, Antibiotic Sensitivity, and Virulence – Yi-Wei Chen – mBio

Preprint: Genomic and ecologic characteristics of the airway microbial-mucosal complex – Leah Cuthbertson – BioXriv 

Beneficial Microbes and Compounds

Lactiplantibacillus plantarum Regulated Intestinal Microbial Community and Cytokines to Inhibit Salmonella typhimurium Infection – Rui-Han Liu – Probiotics and Antimicrobial Proteins

Animal Microbiome

Exploration of rumen microbial and carbohydrate-active enzyme profiles in cattle fed coir a lignin-rich diet using a metagenomic approach – Munni Khatoon – Gene

Plant Microbiome

The core bacterial microbiome of banana (Musa spp.) – Henry W G Birt – Environmental Microbiome

Higher pH is associated with enhanced co-occurrence network complexity, stability and nutrient cycling functions in the rice rhizosphere microbiome – Yaping Guo – Environmental Microbiology

Environmental Microbiology

Virome analysis in lakes of the South Shetland Islands, Antarctica – 2020 – Tatiana Prado – The Science of the Total Environment

Bioinformatics and Microbiome Analysis

Investigating differential abundance methods in microbiome data: A benchmark study – Marco Cappellato – PLoS Computational Biology

A rapid and standardized workflow for functional assessment of bacterial biosensors in fecal samples – Ana Zúñiga – Frontiers in Bioengineering and Biotechnology