Literature

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 info@cosmosid.com.

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Endometriosis specific vaginal microbiota links to urine and serum N-glycome

October 2024

Microbial imbalance in Darier disease: Dominance of various staphylococcal species and absence of Cutibacteria

October 2024

Visceral adiposity in postmenopausal women is associated with a pro-inflammatory gut microbiome and immunogenic metabolic endotoxemia

October 2024

Investigation into the supplementation of a ferric sillen core-linked polymer on the health and physiological performance of broiler chickens

October 2024

Exploring the dichotomy: Shotgun metagenomics reveals diversity of beneficial and pathogenic protist community in arid wetlands of northeastern South Africa

October 2024

Microbial laden mobile phones from international conference attendees pose potential risks to public health and biosecurity

September 2024

Functional Muffins Exert Bifidogenic Effects along with Highly Product-Specific Effects on the Human Gut Microbiota Ex Vivo

September 2024

Metabolite-based inter-kingdom communication controls intestinal tissue recovery following chemotherapeutic injury

September 2024

Dysregulated NOX1-NOS2 activity as hallmark of ileitis in mice

September 2024

Dietary fiber promotes antigen presentation on intestinal epithelial cells and development of small intestinal CD4+CD8αα+ intraepithelial T cells

September 2024

Effect of Topical Microencapsulated Benzoyl Peroxide on the Skin Microbiome in Rosacea: A Randomized, Double-Blind, Crossover, Vehicle-Controlled Clinical Trial

August 2024

Protection against fibrosis by a bacterial consortium in metabolic dysfunction-associated steatohepatitis and the role of amino acid metabolism

August 2024

Impact of obesity on the perinatal vaginal environment and bacterial microbiome: effects on birth outcomes

August 2024

Gut phageome in Mexican Americans: a population at high risk for metabolic dysfunction-associated steatotic liver disease and diabetes

August 2024

Gulf War Illness Is Associated with Host Gut Microbiome Dysbiosis and Is Linked to Altered Species Abundance in Veterans from the BBRAIN Cohort

August 2024

Functional Muffins Exert Bifidogenic Effects along with Highly Product-Specific Effects on the Human Gut Microbiota Ex Vivo

September 2024

Metabolite-based inter-kingdom communication controls intestinal tissue recovery following chemotherapeutic injury

September 2024

Dysregulated NOX1-NOS2 activity as hallmark of ileitis in mice

September 2024

Dietary fiber promotes antigen presentation on intestinal epithelial cells and development of small intestinal CD4+CD8αα+ intraepithelial T cells

September 2024

Effect of Topical Microencapsulated Benzoyl Peroxide on the Skin Microbiome in Rosacea: A Randomized, Double-Blind, Crossover, Vehicle-Controlled Clinical Trial

August 2024

Protection against fibrosis by a bacterial consortium in metabolic dysfunction-associated steatohepatitis and the role of amino acid metabolism

August 2024

Impact of obesity on the perinatal vaginal environment and bacterial microbiome: effects on birth outcomes

August 2024

Gut phageome in Mexican Americans: a population at high risk for metabolic dysfunction-associated steatotic liver disease and diabetes

August 2024

Gulf War Illness Is Associated with Host Gut Microbiome Dysbiosis and Is Linked to Altered Species Abundance in Veterans from the BBRAIN Cohort

August 2024

Draft genome sequence data of Lactiplantibacillus plantarum 33C isolated from Lithuanian fermented food

August 2024

Double-blind randomized placebo-controlled supplementation of a standardized Terminalia chebula fruit extract alters the gut microbiome, phageome, and increases short chain fatty acids in High-BMI, borderline diabetic females

August 2024

The Roles of a Multidrug-Resistant Klebsiella pneumoniae High-Risk Clone and Its Resistance Plasmids on the Gastrointestinal Colonization and Host-Defense Effectors in the Gut

July 2024

A synbiotic of Anaerostipes caccae and lactulose prevents and treats food allergy in mice

July 2024

Microbial diversity, genomics, and phage-host interactions of cyanobacterial harmful algal blooms

July 2024

Environmentally Relevant Antibiotic Concentrations Exert Stronger Selection Pressure on River Biofilm Resistomes than AMR-Reservoir Effluents

June 2024

Revealing the diversity of Jojoba-associated fungi using amplicon metagenome approach and assessing the in vitro biocontrol activity of its cultivable community

May 2024

Co-Removal of Perfluorooctanoic Acid and Nitrate from Water by Coupling Pd Catalysis with Enzymatic Biotransformation

May 2024

Whole-Genome Shotgun Metagenomic Sequencing Reveals Shifts in the Skin Microbiome and Bacteriophages of Psoriasis: An Extended Analysis of Published Data

May 2024

The Nasal Mucosa of the CFTR-KO Mouse Mimics Baseline Cystic Fibrosis Immune Dysregulation and Microbiome Dysbiosis

February 2024

Changes in HLA-B27 Transgenic Rat Fecal Microbiota Following Tofacitinib Treatment and Ileocecal Resection Surgery: Implications for Crohn’s Disease Management

February 2024

Prescription opioids induced microbial dysbiosis worsens severity of chronic pancreatitis and drives pain hypersensitivity

February 2024

Supplemented Infant Formula and Human Breast Milk Show Similar Patterns in Modulating Infant Microbiota Composition and Function In Vitro

February 2024

Alpha-synuclein overexpression can drive microbiome dysbiosis in mice

February 2024

The Impact of In-Water vs. In-Feed Chlortetracycline and Tiamulin Administration in Piglets on the Fecal Prevalence and Antimicrobial Resistance of Salmonella

January 2024

Metagenomic Assessment of the Bacterial Breastfeeding Microbiome in Mature Milk Across Lactation

November 2023

Sediment microbiome diversity and functional profiles of unprotected arid-tropical natural wetlands in South Africa revealed by shotgun metagenomics data

October 2023

Sensitization of Gram-Negative Bacteria to Aminoglycosides with 2-Aminoimidazole Adjuvants

October 2023

Identifying Biodegradation Pathways of Cetrimonium Bromide (CTAB) Using Metagenome, Metatranscriptome, and Metabolome Tri-omics Integration

September 2023

Correlating the Gut Microbiota and Circulating Hormones with Acne Lesion Counts and Skin Biophysical Features

August 2023

A gut-restricted glutamate carboxypeptidase II inhibitor reduces monocytic inflammation and improves preclinical colitis

August 2023

Efficacy and dose response of Lactiplantibacillus plantarum in diarrhea-predominant irritable bowel syndrome Martoni CJ, Srivastava S, Damholt A, Leyer GJ. Efficacy and dose response of Lactiplantibacillus plantarum in diarrhea-predominant irritable bowel syndrome. World J Gastroenterol 2023; 29(28): 4451-4465 [DOI: 10.3748/wjg.v29.i28.4451]

July 2023

Effect of in-water administration of quorum system inhibitors in broilers’ productive performance and intestinal microbiome in a mild necrotic enteritis challenge

July 2023

Whole-genome sequencing and annotation of selected Enterobacteriaceae derived from commercial cucumber fermentation

July 2023

Dynamic effects of probiotic formula ecologic®825 on human small intestinal ileostoma microbiota: a network theory approach

July 2023

Shotgun metagenomic sequencing on skin microbiome indicates dysbiosis exists prior to the onset of atopic dermatitis

July 2023

Interactions between Bifidobacterium and Bacteroides and human milk oligosaccharides and their associations with infant cognition

June 2023

Skin maturation from birth to 10 years of age: Structure, function, composition and microbiome

June 2023

Significant Microbial Changes Are Evident in the Reproductive Tract of Pregnant Rhesus Monkeys at Mid-Gestation but Their Gut Microbiome Does Not Shift until Late Gestation

June 2023

Low-dose glyphosate exposure alters gut microbiota composition and modulates gut homeostasis

June 2023

Wastewater monitoring for detection of public health markers during the COVID-19 pandemic: Near-source monitoring of schools in England over an academic year

May 2023

Shared and Distinct Gut Microbial Profiles in Saudi Women with Metabolically Healthy and Unhealthy Obesity

May 2023

Th17 cells sense microbiome to promote depressive-like behaviors

April 2023

Whole-Genome Sequencing and Annotation of Pediococcus ethanolidurans and Pediococcus pentosaceus Isolates from Commercial Cucumber Fermentation

April 2023

Mutant and curli-producing E. coli enhance the disease phenotype in a hSOD1-G93A mouse model of ALS

April 2023

AN ALGEBRAIC DISCUSSION OF BISEXUAL POPULATIONS WITH WOLBACHIA INFECTION II: EVOLUTION ALGEBRA APPROACH

April 2023

Fermentation of the Brown Seaweed Alaria esculenta by a Lactic Acid Bacteria Consortium able to Utilize Mannitol and Laminari-Oligosaccharides

April 2023

Pilot characterization of the salivary microbiome in pediatric cancer patients

April 2023

HMOs Exert Marked Bifidogenic Effects on Children’s Gut Microbiota Ex Vivo, Due to Age-Related Bifidobacterium Species Composition

April 2023

Metagenomic Shotgun Sequencing Reveals Specific Human Gut Microbiota Associated with Insulin Resistance and Body Fat Distribution in Saudi Women

April 2023

Lacticaseibacillus rhamnosus ATCC 53103 and Limosilactobacillus reuteri ATCC 53608 Synergistically Boost Butyrate Levels upon Tributyrin Administration Ex Vivo

March 2023

Study design and methods for the pilot study of muscadine grape extract supplement to improve fatigue among older adult cancer survivors (FOCUS) trial

March 2023

Effect of a Fructose-Rich Diet on Gut Microbiota and Immunomodulation: Potential Factors for Multiple Sclerosis

March 2023

Dectin-1 signaling on colonic γδ T cells promotes psychosocial stress responses

March 2023

Ketogenic diet therapy for pediatric epilepsy is associated with alterations in the human gut microbiome that confer seizure resistance in mice

March 2023

Genome Analysis of Two Pseudomonas syringae pv. aptata Strains with Different Virulence Capacity Isolated from Sugar Beet: Features of Successful Pathogenicity in the Phyllosphere Microbiome

February 2023

Probiotics supplementation to adult human small intestinal stoma microbiota causes dynamic increase in the community resistance to perturbations and nutrient utilization

January 2023

Serum Vitamin D Level and Gut Microbiota in Women

January 2023

Potential reservoirs of antimicrobial resistance in livestock waste and treated wastewater that can be disseminated to agricultural land

Janaury 2023

Capacity of a Microbial Synbiotic To Rescue the In Vitro Metabolic Activity of the Gut Microbiome following Perturbation with Alcohol or Antibiotics

January 2023

Fast Track Diagnostic Tools for Clinical Management of Sepsis: Paradigm Shift from Conventional to Advanced Methods

January 2023

The role of environmental enrichment in the aetiopathogenesis of Staphylococcus aureus facial, periorbital and retroorbital abscesses in mice

Janaury 2023

Change and stasis of distinct sediment microbiomes across Port Everglades Inlet (PEI) and the adjacent coral reefs

January 2023

Dietary Polyphenols in Relation to Gut Microbiota Composition in Saudi Arabian Females

December 2022

Human blood vessel microbiota in healthy adults based on common femoral arteries of brain-dead multi-organ donors

November 2022

Vitamin B12 Status and Gut Microbiota among Saudi Females with Obesity

November 2022

Metagenomics of Parkinson's disease implicates the gut microbiome in multiple disease mechanisms

November 2022

Dynamics of Fecal Antimicrobial Resistance in the Young Dairy Calf

October 2022

Impact of gut permeability on the breast microbiome using a non-human primate model

Alaa Bawaneh, , Carol A. Shively, Janet Austin Tooze and Katherine Loree Cook October 2022

Influence of Adiposity on the Gut Microbiota Composition of Arab Women: A Case-Control Study

Esra’a A. Aljazairy, Sara Al-Musharaf, Manal Abudawood, Basmah Almaarik, Syed D. Hussain, Abdullah M. Alnaami, Shaun Sabico, Nasser M. Al-Daghri, Mario Clerici and Ghadeer S. Aljuraiban October 2022

Assembly of Olivibacter sp. Strain UJ_SKK_5.1 Genome Sequence, Isolated from Metagenomes of Macrotermes bellicosus Guts Collected from Hot, Arid Nigeria

Richard J. Kutshik, Bitrus Yakubu, Enoch B. Joel, Jessica L. Lenka, Aminu Tukur, Ishaya Y. Longdet September 2022

Dietary Isoflavones Alter Gut Microbiota and Lipopolysaccharide Biosynthesis to Reduce Inflammation

Sudeep Ghimire, Nicole M. Cady, Peter Lehman, Stephanie R. Peterson, Shailesh K. Shahi, Faraz Rashid, Shailendra Giri & Ashutosh K. Mangalam September 2022

The Role of Multiple Sclerosis Therapies on the Dynamic of Human Gut Microbiota

Vacaras V, Muresanu DF, Buzoianu A, Nistor C, Vesa SC, Paraschiv AC, Botos-Vacaras D, Vacaras C, Vithoulkas G September 2022

Oral ingestion of the environmental toxicant trichloroethylene in rats induces alterations in the gut microbiome: Relevance to idiopathic Parkinson's disease

September 2022

Exposure to crop production alters cecal prokaryotic microbiota, inflates virulome and resistome in wild prairie grouse

August 2022

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

Complex and unexpected outcomes of antibiotic therapy against a polymicrobial infection

May 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

Gut Microbiome Alterations Associated with Diabetes in Mexican Americans in South Texas

April 2022

Gut microbiome features associated with liver fibrosis in Hispanics, a population at high risk for fatty liver disease

April 2022

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

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

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