At CosmosID, we are passionate about science and publishing the most up-to-date research in the microbiome space. Our literature library below features recent findings from our clients using our CosmosID-HUB pipeline.

Explore the range of topics our clients work in, from studies on the oral microbiota of dogs to waste water microbiota, human disease, and much more.

Interested in a specific topic and looking for literature? Please reach out to us at

Draft Genome Sequence of Lysinibacillus sp. Strain BPa_S21, Isolated from Petroleum-Contaminated Soil in Delta State, Nigeria
Grace A. Okenmor, Richard J. Kutshik, Ishaya Y. Longdet July 2022
Bladder Tissue Microbiome Composition in Patients of Bladder Cancer or Benign Prostatic Hyperplasia and Related Human Beta Defensin Levels
Bassel Mansour, Ádám Monyók, Márió Gajdács, Balázs Stercz, Nóra Makra, Kinga Pénzes, István Vadnay, Dóra Szabó and Eszter Ostorházi July 2022
Absence of toxin gene transfer from Clostridioides difficile strain 630Δerm to nontoxigenic C. difficile strain NTCD-M3r in filter mating experiments
Susan P. Sambol,Stuart Johnson,Adam Cheknis,Dale N. Gerding June 2022
Mobile phones are hazardous microbial platforms warranting robust public health and biosecurity protocols
Matthew Olsen, Rania Nassar, Abiola Senok, Susan Moloney, Anna Lohning, Peter Jones, Gary Grant, Mark Morgan, Dinesh Palipana, Simon McKirdy, Rashed Alghafri & Lotti Tajouri June 2022
Host gut resistome in Gulf War chronic multisymptom illness correlates with persistent inflammation
Dipro Bose, Somdatta Chatterjee, Ethan Older, Ratanesh Seth, Patricia Janulewicz, Punnag Saha, Ayan Mondal, Jeffrey M. Carlson, Alan W. Decho, Kimberly Sullivan, Nancy Klimas, Stephen Lasley, Jie Li & Saurabh Chatterjee June 2022
Oral Microbiota Populations of Adult Dogs Consuming Wet or Dry Foods
Patrícia M Oba, Kelly M Sieja, Stephanie C J Keating, Teodora Hristova, Amy J Somrak, Kelly S Swanson May 2022
Inulin Supplementation Mitigates Gut Dysbiosis and Brain Impairment Induced by Mild Traumatic Brain Injury during Chronic Phase
Lucille M. Yanckello, Brian Fanelli, Scott McCulloch, Xin Xing, McKenna Sun, Tyler C. Hammond, Rita Colwell, Zezong Gu, Aaron C. Ericsson, Ya-Hsuan Chang, Adam D. Bachstetter, Ai-Ling Lin March 2022
The Neuro-Endo-Microbio-Ome Study: A Pilot Study of Neurobiological Alterations Pre- Versus Post-Bariatric Surgery
Khushbu Agarwal, PhD, Katherine A. Maki, PhD, Carlotta Vizioli, PhD, Susan Carnell, PhD, Ethan Goodman, PhD, Matthew Hurley, PhD, Civonnia Harris, BSc, Rita Colwell, PhD, Kimberley Steele, MD, PhD, Paule V. Joseph, PhD April 2022
Genome Sequences for Levilactobacillus brevis Autochthonous to Commercial Cucumber Fermentations
Clinton A. Page, Ruby A. Carter-Ogden, Alice M. Lee, Ilenys M. Pérez-Díaz April 2022
Analysis of the Ability of Capsaicin to Modulate the Human Gut Microbiota In Vitro
Karley K. Mahalak, Jamshed Bobokalonov, Jenni Firrman, Russell Williams, Bradley Evans, Brian Fanelli, Jason W. Soares, Masuko Kobori and LinShu Liu March 2022
Metagenomic Characterization of The Tracheobronchial Microbiome in Lung Cancer
Stephanie Hogue, Christine M. Pierce, Shirlene Paul, Ram Thapa, Youngchul Kim, Lary A. Robinson December 21
Antibiotics and fecal transfaunation differentially affect microbiota recovery, associations, and antibiotic resistance in lemur guts
Sally L. Bornbusch, Rachel L. Harris, Nicholas M. Grebe, Kimberly Roche, Kristin Dimac-Stohl & Christine M. Drea October 2021
Dysbiosis of the gut microbiome impairs mouse skeletal muscle adaptation to exercise
Taylor R. Valentino, Ivan J. Vechetti Jr, C. Brooks Mobley ,Cory M. Dungan ,Lesley Golden, Jensen Goh, John J. McCarthy September 2021
Metagenomics of Plant Rhizosphere and Endophytic Association: Concepts and Applications
Arpita Ghosh, Ankita Rathore & Balakuntla Jayanth September 21
Piglet Gut and in-Barn Manure from Farms on a Raised without Antibiotics Program Display Reduced Antimicrobial Resistance but an Increased Prevalence of Pathogens
Samuel M. Chekabab, John R. Lawrence, Alvin C. Alvarado, Bernardo Z. Predicala and Darren R. Korber September 2021
Gut microbiota signatures are associated with toxicity to combined CTLA-4 and PD-1 blockade
Miles C. Andrews, Connie P. M. Duong, Jennifer A. Wargo July 2021
Human beta defensin levels and vaginal microbiome composition in post-menopausal women diagnosed with lichen sclerosus
Alexandra Brunner, Márta Medvecz, Nóra Makra, Miklós Sárdy, Kinga Komka, Máté Gugolya, Dóra Szabó, Márió Gajdács & Eszter Ostorházi Auig 21
A pilot metagenomic study reveals that community derived mobile phones are reservoirs of viable pathogenic microbes
Matthew Olsen, Rania Nassar, Abiola Senok, Abdulla Albastaki, John Leggett, Anna Lohning, Mariana Campos, Peter Jones, Simon McKirdy, Lotti Tajouri & Rashed Alghafri July 2021
Bacteria - derived short chain fatty acids restore sympathoadrenal responsiveness to hypoglycemia after antibiotic-induced gut microbiota depletion
Edmund F. LaGamma Furong Hua Fernando Pena Cruz Philip Bouchevc Bistra B.Nankova July 2021
Microbiota and Metabolomic Patterns in the Breast Milk of Subjects with Celiac Disease on a Gluten-Free Diet
Katherine L. Olshan , Ali R. Zomorrodi, Meritxell Pujolassos, Jacopo Troisi, Nayeim Khan, Brian Fanelli, Victoria Kenyon, Alessio Fasano andMaureen M. Leonard Jun 21
Microbiome signatures of progression toward celiac disease onset in at-risk children in a longitudinal prospective cohort study
Maureen M. Leonard, Francesco Valitutti, Hiren Karathia, Meritxell Pujolassos, Victoria Kenyon, Brian Fanelli, Jacopo Troisi, Poorani Subramanian, Stephanie Camhi, Angelo Colucci, Gloria Serena, Salvatore Cucchiara, Chiara Maria Trovato, Basilio Malamisura, Ruggiero Francavilla, Luca Elli, Nur A. Hasan, Ali R. Zomorrodi, Rita Colwell, Alessio Fasano, and The CD-GEMM Team. July 2021
Gut microbiota of frugo-folivorous sifakas across environments.
Greene LK, Blanco MB, Rambeloson E, Graubics K, Fanelli B, Colwell RR, Drea CM. May 2021
Diversity of Plasmids and Genes Encoding Resistance to Extended-Spectrum β-Lactamase in Escherichia coli from Different Animal Sources.
Ibekwe A, Durso L, Ducey TF, Oladeinde A, Jackson CR, Frye JG, Dungan R, Moorman T, Brooks JP, Obayiuwana A, Karathia H, Fanelli B, Hasan N.
Diet, obesity, and the gut microbiome as determinants modulating metabolic outcomes in a non-human primate model.
Newman TM, Shively CA, Register TC, Appt SE, Yadav H, Colwell RR, Fanelli B, Dadlani M, Graubics K, Nguyen UT, Ramamoorthy S, Uberseder B, Clear KYJ, Wilson AS, Reeves KD, Chappell MC, Tooze JA, Cook KL. May 2021
Spinal Cord Injury Changes the Structure and Functional Potential of Gut Bacterial and Viral Communities
Jingjie Du, Ahmed A. Zayed, Kristina A. Kigerl, Kylie Zane, Matthew B. Sullivan sullivan, and Phillip G. Popovich . Mayb2021
Assessing the effects of common topical exposures on skin bacteria associated with atopic dermatitis
C. R. Castillo, M. E. Alishahedani, P. Gough, P. P. Chaudhary, M. Yadav, J. Matriz, I. A. Myles. May 2021
A New Strain of Christensenella minuta as a Potential Biotherapy for Obesity and Associated Metabolic Diseases
Wilfrid Mazier,Katy Le Corf, Ccori Martinez, Héloïse Tudela, Déborah Kissi, Camille Kropp, Chrislain Coubard, Marion Soto, Frédéric Elustondo, Georges Rawadi and Sandrine P. Claus. Apr 2021
Aging-Induced Dysbiosis of Gut Microbiota as a Risk Factor for Increased Listeria monocytogenes Infection.
Alam MS, Gangiredla J, Hasan NA, Barnaba T, Tartera C. Apr 21
Fungal Dysbiosis in Children with Celiac Disease.
El Mouzan M, Al-Hussaini A, Fanelli B, Assiri A, AlSaleem B, Al Mofarreh M, Al Sarkhy A, Alasmi M. Mar 21
The genital microbiome and its potential for detecting sexual assault
Mirna Ghemrawi, Andrea Ramírez Torres, George Duncan, Rita Colwell, Manoj Dadlani, Bruce McCord. Mar 21
Evaluation of a Combined Multilocus Sequence Typing and Whole-Genome Sequencing Two-Step Algorithm for Routine Typing of Clostridioides difficile
Mini Kamboj, Tracy McMillen, Mustafa Syed, Hoi Yan Chow, Krupa Jani, Anoshe Aslam, Jennifer Brite, Brian Fanelli, Nur A Hasan, Manoj Dadlani, Lars Westblade, Ahmet Zehir, Matthew Simon, N Esther Babady. Jan 21
Water Microbiota from a Commercial Alfalfa Sprout Crop over 4 Days of Growth.
Reed E, Sanderson R, Sanderson B, Ramachandran P, Commichaux S, Brown E, Zheng J, Strain E, Ottesen A. Jan 21
Vaccine Hyporesponse Induced By Individual Antibiotic Treatment In Mice And Non-Human Primates Is Diminished Upon Recovery Of The Gut Microbiome
Gokul Swaminathan, Michael Citron, Jianying Xiao, James E Norton Jr, Abigail L Reens, Begüm D. Topçuoğlu, Julia M Maritz, Keun-Joong Lee, Daniel C Freed, Teresa M Weber, Cory H White, Mahika Kadam, Erin Spofford, Erin Bryant-Hall, Gino Salituro, Sushma Kommineni, Xue Liang, Olga Danilchanka, Jane A Fontenot, Christopher H Woelk, Dario A Gutierrez, Daria J Hazuda, Geoffrey D Hannigan. Jan 21
Temporal Resistome and Microbial Community Dynamics in an Intensive Aquaculture Facility with Prophylactic Antimicrobial Treatment.
Patil HJ, Gatica J, Zolti A, Benet-Perelberg A, Naor A, Dror B, Al Ashhab A, Marman S, Hasan NA, Colwell RR, Sher D, Minz D, Cytryn E. Dec 20
Metagenomic Next-Generation Sequencing of Nasopharyngeal Specimens Collected from Confirmed and Suspect COVID-19 Patients.
Mostafa HH, Fissel JA, Fanelli B, Bergman Y, Gniazdowski V, Dadlani M, Carroll KC, Colwell RR, Simner PJ. Nov 20
Feasibility and Comparison Study of Fecal Sample Collection Methods in Healthy Volunteers and Solid Organ Transplant Recipients Using 16S rRNA and Metagenomics Approaches
Sunil M Kurian, Skyler Gordon, Bethany Barrick, Manoj N Dadlani, Brian Fanelli, Jenny B Cornell, Steven R Head, Christopher L Marsh, Jamie Case. Oct 20
Multi-omics analysis reveals the influence of genetic and environmental risk factors on developing gut microbiota in infants at risk of celiac disease.
Leonard MM, Karathia H, Pujolassos M, Troisi J, Valitutti F, Subramanian P, Camhi S, Kenyon V, Colucci A, Serena G, Cucchiara S, Montuori M, Malamisura B, Francavilla R, Elli L, Fanelli B, Colwell R, Hasan N, Zomorrodi AR, Fasano A; CD-GEMM Team. Sep 20
A New Whole Genome Culture-Independent Diagnostic Test (WG-CIDT) for Rapid Detection of Salmonella in Lettuce.
Ogunremi D, Dupras AA, Naushad S, Gao R, Duceppe MO, Omidi K, Márquez IG, Huang H, Goodridge L, Lévesque RC, Hasan NA, Dadlani M, Dixon B, Magierowski S, Masson L. Apr 20
A comparative analysis of drinking water employing metagenomics.
Brumfield KD, Hasan NA, Leddy MB, Cotruvo JA, Rashed SM, Colwell RR, Huq A. Apr 20
Microbial resolution of whole genome shotgun and 16S amplicon metagenomic sequencing using publicly available NEON data.
Brumfield KD, Huq A, Colwell RR, Olds JL, Leddy MB. Feb 20
Comparison of Three Commercial Tools for Metagenomic Shotgun Sequencing Analysis
Matthew Thoendel, Patricio Jeraldo, Kerryl E Greenwood-Quaintance, Janet Yao, Nicholas Chia, Arlen D Hanssen, Matthew P Abdel, Robin Patel. Feb 20
Bacterial, Gut Microbiome-Modifying Therapies to Defend against Multidrug Resistant Organisms
Amy Feehan, Julia Garcia-Diaz. Jan 20
Multiple NDM-5 Expressing Escherichia Coli Isolates From An Immunocompromised Pediatric Host
Flerlage, et al, University of Tennessee Health Science Center, January 2020 Open Forum Infectious Diseases
Gut DNA Virome Diversity And Its Association With Host Bacteria Regulate Inflammatory Phenotype And Neuronal Immunotoxicity In Experimental Gulf War Illness
Ratanesh, S et al, University of South Carolina, Oct 2019, Viruses
Metagenomics-Based Evaluation Of Groundwater Microbial Profiles In Response To Treated Wastewater Discharge
Zaouri et al, WDRC October 2019, Elsevier
Prosthetic Joint Infections Present Diverse And Unique Microbial Communities Using Combined Whole-Genome Shotgun Sequencing And Culturing Methods
Weaver, et al., University of Notre Dame Oct 2019 Journal of Medical Microbiology
Resistome Metagenomics From Plate To Farm: The Resistome And Microbial Composition During Food Waste Feeding And Composting On A Vermont Poultry Farm
Eckstrom, K and Barlow, J.W., University of Vermont July 2019 bioRxiv Preprint
Oral Beta-Lactamase Protects The Canine Gut Microbiome From Oral Amoxicillin-Mediated Damage
Connelly, et al., Synthetic Biologics May 2019 Microorganisms
Drinking Water Microbiome Project: Is It Time?
Hull, N.M. et al, Ohio State University Apr 2019, Trends in Microbiology
Strain- And Species-Level Variation In The Microbiome Of Diabetic Wounds Is Associated With Clinical Outcomes And Therapeutic Efficacy
Kalan, L. et al, May 2019, Cell Host & Microbe.
Metagenomic Profiling Of Microbial Pathogens In The Little Bighorn River, Montana
Hamner, S. et al, March 2019 International Journal of Environmental Research and Public Health.
Microbiota Of The Hickey Run Tributary Of The Anacostia River
Cagle, R. et al, US FDA March 2019 Microbiology Resource Announcements
Oral Metallo-Beta-Lactamase Protects The Gut Microbiome From Carbapenem-Mediated Damage And Reduces Propagation Of Antibiotic Resistance In Pigs
Connelly et al, Synthetic Biologics February 2019 Frontiers in Microbiology
Genome Sequence Of Enterococcus Faecalis NVIT04, Isolated From Nasonia Vitripennis
Wang, GH. et al, The Rowland Institute at Harvard University January 2019 American Society for Microbiology Microbiology Resource Announcements
Metagenome Sequencing-Based Strain-Level And Functional Characterization Of Supragingival Microbiome Associated With Dental Caries In Children
Al-Hebshi, N. et al, Temple School of Dentistry December 2018 Journal of Oral Microbiology
Evaluation Of The CosmosID Bioinformatics Platform For Prosthetic Joint-Associated Sonicate Fluid Shotgun Metagenomic Data Analysis
Yan, Q. et al, Mayo Clinic November 2018 Journal of Clinical Microbiology
The Microbial Basis Of Impaired Wound Healing: Differential Roles For Pathogens, “Bystanders”, And Strain-Level Diversification In Clinical Outcomes
Kalan, L. et al, University of Wisconsin-Madison September 2018 BioRxiv preprint
Current Progress And Future Opportunities In Applications Of Bioinformatics For Biodefense And Pathogen Detection: Report From The Winter Mid-Atlantic Microbiome Meet-Up
Meisel J. et al, Center for Bioinformatics and Computational Biology, University of Maryland November 2018 Microbiome
Characterization Of The Microbiome At The World’s Largest Potable Water Reuse Facility
Stamps B. et al, Colorado School of Mines October 2018 Frontiers in Microbiology
High-Resolution Microbiome Profiling With Metagenomics Next-Generation Sequencing And CosmosID
Illumina Application Note, 2018.
A Metagenomic Approach To Evaluating Surface Water Quality In Haiti
Roy, M. et al, University of Massachusetts Amherst October 2018 International Journal of Environmental Research and Public Health
Exploring The Microbiome Of Callinectes Sapidus (Maryland Blue Crab)
Ramachandran, P. et al, US FDA May 2018 Microbiology Resource Announcements
The Invasive Brazilian Pepper Tree (Schinus Terebinthifolius) Is Colonized By A Root Microbiome Enriched With Alphaproteobacteria And Unclassified Spartobacteria
Dawkins, K. et al, Florida Atlantic University May 2018 Frontiers in Microbiology
Messages From The Second International Conference On Clinical Metagenomics (ICCMg2)
Ruppe, E. et al, Hôpital Bichat April 2018 Microbes and Infection
Characterization Of The Microbiota Of Oyster Larvae (Crassostrea Virginica) And Tank Water From An Aquaculture System With High And Low Larval Survival Rates
Ramachandran, P. et al, US FDA June 2018 Microbiology Resource Announcements
Comparison Of Infant Gut And Skin Microbiota, Resistome And Virulome Between Neonatal Intensive Care Unit (NICU) Environments
Hourigan, S. et al, Inova Children’s Hospital June 2018 Frontiers in Microbiology
Interrogating The Microbiome: Experimental And Computational Considerations In Support Of Study Reproducibility
Poussin, C. et al, Philip Morris Products S.A. June 2018 Drug Discovery Today
Distinct Consequences Of Amoxicillin And Ertapenem Exposure In The Porcine Gut Microbiome
Connelly, S. et al, Synthetic Biologics April 2018 Anaerobe
The Microbiomes Of Blowflies And Houseflies As Bacterial Transmission Reservoirs
Junqueira, A. et al, Nanyang Technological University Nov 2017 Scientific Reports
10476142 - green celery isolated on white background.
Application Of Next Generation Sequencing Toward Sensitive Detection Of Enteric Viruses Isolated From Celery Samples As An Example Of Produce
Yang, Z. et al, US FDA Nov 2017 International Journal of Food Microbiology
Metagenomic Sequencing To Replace Semi-Quantitative Urine Culture For Detection Of Urinary Tract Infections: A Proof Of Concept
Janes, V. et al, Academic Medical Center Aug 2017 BioRxiv Preprint
Aging-Associated Dysbiosis Increases Susceptibility To Enteric Viral Infection In Drosophila
Sansone, C. et al, University of Pennsylvania June 2017 BioRxiv