Cross-laboratory replication of pseudomyxoma peritonei tumor microbiome reveals reproducible microbial signatures

Authors: Victoria F. Nieciecki, Faith C. Blum, Ryan C. Johnson, Traci L. Testerman, Tom J. McAvoy, Mary Caitlin King, Vadim Gushchin, Jeannette M. Whitmire, Kenneth G. Frey, Lindsay Glang, Dessiree Peña-Gomez, Kimberly A. Bishop-Lilly, Armando Sardi, D. Scott Merrell, Jessica L. Metcalf

Source: mSphere, Vol 10, Iss 3 (2025)

Subject Terms: reproducibility, contamination, amplicon sequencing, source tracking, Pseudomyxoma Peritonei, colorectal cancer, Microbiology, QR1-502

File Description: electronic resource

Relation: https://doaj.org/toc/2379-5042

Access URL: https://doaj.org/article/87998d7cbf444b22ae2ae22061c4c4b0

Stochasticity Highlights the Development of Both the Gastrointestinal and Upper-Respiratory-Tract Microbiomes of Neonatal Dairy Calves in Early Life

Authors: A. Nathan Frazier, Logan Ferree, Aeriel D. Belk, Khalid Al-Lakhen, M. Caitlin Cramer, Jessica L. Metcalf

Source: Animals, Vol 15, Iss 3, p 361 (2025)

Subject Terms: microbial ecology, dairy calf, disease, stochasticity, determinism, Veterinary medicine, SF600-1100, Zoology, QL1-991

File Description: electronic resource

Relation: https://www.mdpi.com/2076-2615/15/3/361; https://doaj.org/toc/2076-2615

Access URL: https://doaj.org/article/ce464fca9fba48fa973dc27e18389e47

Time to rethink academic publishing: the peer reviewer crisis

Authors: Carolina Tropini, B. Brett Finlay, Mark Nichter, Melissa K. Melby, Jessica L. Metcalf, Maria Gloria Dominguez-Bello, Liping Zhao, Margaret J. McFall-Ngai, Naama Geva-Zatorsky, Katherine R. Amato, Eduardo A. Undurraga, Hendrik N. Poinar, Jack A. Gilbert

Source: mBio, Vol 14, Iss 6 (2023)

Subject Terms: peer review, reviewer rewards, artificial intelligence, early career researcher, peer review crisis, Microbiology, QR1-502

File Description: electronic resource

Relation: https://doaj.org/toc/2150-7511

Access URL: https://doaj.org/article/6875683cea994700b14c0a85ec5a39a1

Dietary Polyphenols Support Akkermansia muciniphila Growth via Mediation of the Gastrointestinal Redox Environment

Authors: Charlene B. Van Buiten, Valerie A. Seitz, Jessica L. Metcalf, Ilya Raskin

Source: Antioxidants, Vol 13, Iss 3, p 304 (2024)

Subject Terms: polyphenol, reactive oxygen species, gut microbiome, metabolic syndrome, vitamin, antioxidant, Therapeutics. Pharmacology, RM1-950

File Description: electronic resource

Relation: https://www.mdpi.com/2076-3921/13/3/304; https://doaj.org/toc/2076-3921

Access URL: https://doaj.org/article/d42496c0ff5a45c9b1881ee2b93d4ab5

Resistomes and microbiome of meat trimmings and colon content from culled cows raised in conventional and organic production systems

Authors: Margaret D. Weinroth, Kevin M. Thomas, Enrique Doster, Amit Vikram, John W. Schmidt, Terrance M. Arthur, Tommy L. Wheeler, Jennifer K. Parker, Ayanna S. Hanes, Najla Alekoza, Cory Wolfe, Jessica L. Metcalf, Paul S. Morley, Keith E. Belk

Source: Animal Microbiome, Vol 4, Iss 1, Pp 1-16 (2022)

Subject Terms: Antibiotic resistance, 16S, Target-enriched metagenomics, Microbiome, Bovine, Veterinary medicine, SF600-1100, Microbiology, QR1-502

File Description: electronic resource

Relation: https://doaj.org/toc/2524-4671

Access URL: https://doaj.org/article/67b11103e1e94d78b62a844c46b4f362

A Pilot Study: the Development of a Facility-Associated Microbiome and Its Association with the Presence of Listeria Spp. in One Small Meat Processing Facility

Authors: Aeriel D. Belk, A. Nathan Frazier, Luke K. Fuerniss, Robert Delmore, Keith Belk, Brad Borlee, Ifigenia Geornaras, Jennifer N. Martin, Jessica L. Metcalf

Source: Microbiology Spectrum, Vol 10, Iss 5 (2022)

Subject Terms: Listeria, Listeria monocytogenes, built environment, food safety, meat processing, microbiome, Microbiology, QR1-502

File Description: electronic resource

Relation: https://doaj.org/toc/2165-0497

Access URL: https://doaj.org/article/497aa55e22df43c8a64f6042d38af82d

Interrelated Effects of Zinc Deficiency and the Microbiome on Group B Streptococcal Vaginal Colonization

Authors: Lindsey R. Burcham, Zachary M. Burcham, Madeline S. Akbari, Jessica L. Metcalf, Kelly S. Doran

Source: mSphere, Vol 7, Iss 4 (2022)

Subject Terms: vaginal colonization, dietary zinc, vaginal microbiome, Streptococcus agalactiae, group B Streptococcus, GBS, Microbiology, QR1-502

File Description: electronic resource

Relation: https://doaj.org/toc/2379-5042

Access URL: https://doaj.org/article/e74cf92255564858a5a33818f540616c

Bacteroidetes and Firmicutes Drive Differing Microbial Diversity and Community Composition Among Micro-Environments in the Bovine Rumen

Authors: Lee J. Pinnell, Arquimides A. Reyes, Cory A. Wolfe, Maggie D. Weinroth, Jessica L. Metcalf, Robert J. Delmore, Keith E. Belk, Paul S. Morley, Terry E. Engle

Source: Frontiers in Veterinary Science, Vol 9 (2022)

Subject Terms: 16S rRNA gene sequencing, cattle, rumen, microbiome, core microbial community, Veterinary medicine, SF600-1100

File Description: electronic resource

Relation: https://www.frontiersin.org/articles/10.3389/fvets.2022.897996/full; https://doaj.org/toc/2297-1769

Access URL: https://doaj.org/article/1a35662b3e984d58836f4816e6af33cd

Convergence of human and Old World monkey gut microbiomes demonstrates the importance of human ecology over phylogeny

Authors: Katherine R. Amato, Elizabeth K. Mallott, Daniel McDonald, Nathaniel J. Dominy, Tony Goldberg, Joanna E. Lambert, Larissa Swedell, Jessica L. Metcalf, Andres Gomez, Gillian A. O. Britton, Rebecca M. Stumpf, Steven R. Leigh, Rob Knight

Source: Genome Biology, Vol 20, Iss 1, Pp 1-12 (2019)

Subject Terms: Human gut microbiome, Primate gut microbiome, Cercopithecine, Human evolution, Biology (General), QH301-705.5, Genetics, QH426-470

File Description: electronic resource

Relation: http://link.springer.com/article/10.1186/s13059-019-1807-z; https://doaj.org/toc/1474-760X

Access URL: https://doaj.org/article/51e72d4c0c70424ea8b9930380229b07

A Pilot Study of Microbial Succession in Human Rib Skeletal Remains during Terrestrial Decomposition

Authors: Heather Deel, Alexandra L. Emmons, Jennifer Kiely, Franklin E. Damann, David O. Carter, Aaron Lynne, Rob Knight, Zhenjiang Zech Xu, Sibyl Bucheli, Jessica L. Metcalf

Source: mSphere, Vol 6, Iss 4 (2021)

Subject Terms: Microbiology, QR1-502

File Description: electronic resource

Relation: https://doaj.org/toc/2379-5042

Access URL: https://doaj.org/article/4844f865806f4e458f1627b6073f133e

Air versus Water Chilling of Chicken: a Pilot Study of Quality, Shelf-Life, Microbial Ecology, and Economics

Authors: Aeriel D. Belk, Toni Duarte, Casey Quinn, David A. Coil, Keith E. Belk, Jonathan A. Eisen, Jason C. Quinn, Jennifer N. Martin, Xiang Yang, Jessica L. Metcalf

Source: mSystems, Vol 6, Iss 2 (2021)

Subject Terms: chicken, meat, chilling methods, spoilage, shelf life, 16S rRNA gene, Microbiology, QR1-502

File Description: electronic resource

Relation: https://doaj.org/toc/2379-5077

Access URL: https://doaj.org/article/8d4f5c6cf4014279a2c81ce2b8209ccc

Air versus Water Chilling of Chicken: a Pilot Study of Quality, Shelf-Life, Microbial Ecology, and Economics

Authors: Aeriel D. Belk, Toni Duarte, Casey Quinn, David A. Coil, Keith E. Belk, Jonathan A. Eisen, Jason C. Quinn, Jennifer N. Martin, Xiang Yang, Jessica L. Metcalf

Source: mSystems, Vol 6, Iss 2 (2021)

Subject Terms: chicken, meat, chilling methods, spoilage, shelf life, 16S rRNA gene, Microbiology, QR1-502

File Description: electronic resource

Relation: https://doaj.org/toc/2379-5077

Access URL: https://doaj.org/article/01b9cdbd54c5439db8baac98756f69f4

Plant Selenium Hyperaccumulation Affects Rhizosphere: Enhanced Species Richness and Altered Species Composition

Authors: Alyssa T. Cochran, Jemma Bauer, Jessica L. Metcalf, Petra Lovecka, Martina Sura de Jong, Sven Warris, Paul J. W. Mooijman, Ingrid van der Meer, Rob Knight, Elizabeth A. H. Pilon-Smits

Source: Phytobiomes Journal, Vol 2, Iss 2, Pp 82-91 (2018)

Subject Terms: Plant culture, SB1-1110, Microbial ecology, QR100-130, Plant ecology, QK900-989

File Description: electronic resource

Relation: https://doaj.org/toc/2471-2906

Access URL: https://doaj.org/article/4e02af3eaa844d50a836d858454ec0b3

Using the gut microbiota as a novel tool for examining colobine primate GI health

Authors: Katherine R. Amato, Jessica L. Metcalf, Se Jin Song, Vanessa L. Hale, Jonathan Clayton, Gail Ackermann, Greg Humphrey, Kefeng Niu, Duoying Cui, Hongxia Zhao, Mark D. Schrenzel, Chia L. Tan, Rob Knight, Josephine Braun

Source: Global Ecology and Conservation, Vol 7, Iss C, Pp 225-237 (2016)

Subject Terms: Colobine, Zoo, Captive, Gut microbiome, Dysbiosis, Ecology, QH540-549.5

File Description: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S2351989416300610; https://doaj.org/toc/2351-9894

Access URL: https://doaj.org/article/74ebcedf1c1d44db8a6517f43468e21a

American Gut: an Open Platform for Citizen Science Microbiome Research

Authors: Daniel McDonald, Embriette Hyde, Justine W. Debelius, James T. Morton, Antonio Gonzalez, Gail Ackermann, Alexander A. Aksenov, Bahar Behsaz, Caitriona Brennan, Yingfeng Chen, Lindsay DeRight Goldasich, Pieter C. Dorrestein, Robert R. Dunn, Ashkaan K. Fahimipour, James Gaffney, Jack A. Gilbert, Grant Gogul, Jessica L. Green, Philip Hugenholtz, Greg Humphrey, Curtis Huttenhower, Matthew A. Jackson, Stefan Janssen, Dilip V. Jeste, Lingjing Jiang, Scott T. Kelley, Dan Knights, Tomasz Kosciolek, Joshua Ladau, Jeff Leach, Clarisse Marotz, Dmitry Meleshko, Alexey V. Melnik, Jessica L. Metcalf, Hosein Mohimani, Emmanuel Montassier, Jose Navas-Molina, Tanya T. Nguyen, Shyamal Peddada, Pavel Pevzner, Katherine S. Pollard, Gholamali Rahnavard, Adam Robbins-Pianka, Naseer Sangwan, Joshua Shorenstein, Larry Smarr, Se Jin Song, Timothy Spector, Austin D. Swafford, Varykina G. Thackray, Luke R. Thompson, Anupriya Tripathi, Yoshiki Vázquez-Baeza, Alison Vrbanac, Paul Wischmeyer, Elaine Wolfe, Qiyun Zhu, Rob Knight

Source: mSystems, Vol 3, Iss 3 (2018)

Subject Terms: citizen science, microbiome, Microbiology, QR1-502

File Description: electronic resource

Relation: https://doaj.org/toc/2379-5077

Access URL: https://doaj.org/article/0301cbad620f4f3490bc93e225ec5d0c

Correction for Morton et al., 'Uncovering the Horseshoe Effect in Microbial Analyses'

Authors: James T. Morton, Liam Toran, Anna Edlund, Jessica L. Metcalf, Christian Lauber, Rob Knight

Source: mSystems, Vol 3, Iss 1 (2018)

Subject Terms: Microbiology, QR1-502

File Description: electronic resource

Relation: https://doaj.org/toc/2379-5077

Access URL: https://doaj.org/article/ecf30cc7360241978dfbd76123abe335

Correction for Morton et al., 'Uncovering the Horseshoe Effect in Microbial Analyses'

Authors: James T. Morton, Liam Toran, Anna Edlund, Jessica L. Metcalf, Christian Lauber, Rob Knight

Source: mSystems, Vol 3, Iss 1 (2018)

Subject Terms: Microbiology, QR1-502

File Description: electronic resource

Relation: https://doaj.org/toc/2379-5077

Access URL: https://doaj.org/article/26eff736d56d493083787fb38d286bab

Uncovering the Horseshoe Effect in Microbial Analyses

Authors: James T. Morton, Liam Toran, Anna Edlund, Jessica L. Metcalf, Christian Lauber, Rob Knight

Source: mSystems, Vol 2, Iss 1 (2017)

Subject Terms: decomposition, horseshoe, microbial ecology, pH, soil, Microbiology, QR1-502

File Description: electronic resource

Relation: https://doaj.org/toc/2379-5077

Access URL: https://doaj.org/article/50b9099cd7e94228ad0ed0893576c690

Balance Trees Reveal Microbial Niche Differentiation

Authors: James T. Morton, Jon Sanders, Robert A. Quinn, Daniel McDonald, Antonio Gonzalez, Yoshiki Vázquez-Baeza, Jose A. Navas-Molina, Se Jin Song, Jessica L. Metcalf, Embriette R. Hyde, Manuel Lladser, Pieter C. Dorrestein, Rob Knight

Source: mSystems, Vol 2, Iss 1 (2017)

Subject Terms: Aitchison geometry, balance trees, compositionality, cystic fibrosis, niche, soil microbiology, Microbiology, QR1-502

File Description: electronic resource

Relation: https://doaj.org/toc/2379-5077

Access URL: https://doaj.org/article/62566cec9f084d41b29fe01975d8c9d1

Preservation Methods Differ in Fecal Microbiome Stability, Affecting Suitability for Field Studies

Authors: Se Jin Song, Amnon Amir, Jessica L. Metcalf, Katherine R. Amato, Zhenjiang Zech Xu, Greg Humphrey, Rob Knight

Source: mSystems, Vol 1, Iss 3 (2016)

Subject Terms: DNA stability, fecal microbiome, sample storage, Microbiology, QR1-502

File Description: electronic resource

Relation: https://doaj.org/toc/2379-5077

Access URL: https://doaj.org/article/94a254eaaa994081816a74cfd1ce0404