Microbiomes and Complex Microbial Communities

Assessing contamination in DNA extraction kits commonly used for microbiome research

Rabasco, J. T., Kisthardt, S. C., Theriot, C. M., & Callahan, B. J. (2025, September 23).

Dietary protein from different sources escapes host digestion and is differentially modified by gut microbiota

Food & Function.

The ecology, evolution, and physiology of Cardinium: a widespread heritable endosymbiont of invertebrates

[Review of ]. FEMS MICROBIOLOGY REVIEWS, 49.

Evaluation of Parallel Accumulation-Serial Fragmentation methods for metaproteomics using a model microbiome

Shreshta, R., Rajczewski, A. T., Do, K., Willets, M., Kleiner, M., Griffin, T. J., & Jagtap, P. D. (2025, August 15).

Root-secreted proteins: an underexplored component of root exudates

Trends in Plant Science.

Characterization of an isobutylene epoxide hydrolase (IbcK) from the isobutylene-catabolizing bacterium <i>Mycolicibacterium</i> sp. ELW1

Faulkner, N. W., Joyce, J. B., Smith, C., Swartz, P., Rose, R. B., Miller, E. S., & Hyman, M. R. (2025, August 26). (M. Vives, Ed.). APPLIED AND ENVIRONMENTAL MICROBIOLOGY, Vol. 8.

Inducible genome-wide mutagenesis for improvement of pDNA production by <i>E. coli</i>

MICROBIAL CELL FACTORIES, 24(1).

How thoughtful experimental design can empower biologists in the omics era

[Review of ]. NATURE COMMUNICATIONS, 16(1).

Differential modulation of post-antibiotic colonization resistance to <i>Clostridioides difficile</i> by two probiotic <i>Lactobacillus</i> strains

Foley, M. H., McMillan, A. S., O'Flaherty, S., Thanissery, R., Vanhoy, M. E., Fuller, M. G., … Theriot, C. M. (2025, July 21). (J. Ravel, Ed.). MBIO, Vol. 7.

<i>Clostridioides difficile</i> toxins alter host metabolic pathway and bile acid homeostasis gene expression in colonic epithelium

Thomas, S. A., Pike, C. M., Perkins, C. E., Brown, S. T., Jaen, X. M. E., McMillan, A. S., & Theriot, C. M. (2025, June 30). INFECTION AND IMMUNITY.

A Minimal Medium for Culturing Maize Root-Associated Microbes Based on a Plant Growth Medium

Garrell, A.-K., Vintila, S., Phillip, H., Beck, A. E., & Kleiner, M. (2025, July 7).

Metaproteomics-based stable isotope fingerprinting links intestinal bacteria to their carbon source and captures diet-induced substrate switching

ISME JOURNAL, 19(1).

<i>In vitro</i> demonstration and <i>in planta</i> characterization of a condensed, reverse TCA (crTCA) cycle

FRONTIERS IN PLANT SCIENCE, 16.

Guidelines for preventing and reporting contamination in low-biomass microbiome studies

Fierer, N., Leung, P. M., Lappan, R., Eisenhofer, R., Ricci, F., Holland, S. I., … Greening, C. (2025, June 20). NATURE MICROBIOLOGY, Vol. 6.

Differential metaproteomics of bacteria grown in vitro and in planta reveals functions used during growth on maize roots

Garrell, A.-K., Cheadle, J., Crook, N., Pal, G., Septer, A. N., Wagner, M. R., … Kleiner, M. (2025, June 2).

Adaptations in gut Bacteroidales facilitate stable co-existence with their lytic bacteriophages

GUT MICROBES, 17(1).

Benchmarking Spectral Library and Database Search Approaches for Metaproteomics Using a Ground-Truth Microbiome Dataset

Rajczewski, A. T., Mehta, S., Wagner, R., Gabriel, W., Johnson, J., Do, K., … Jagtap, P. D. (2025, May 20).

Enabling technologies for<i> in</i><i> situ</i> biomanufacturing using probiotic yeast

[Review of ]. ADVANCED DRUG DELIVERY REVIEWS, 223.

The microbiologist's guide to metaproteomics

Bossche, T. V. D., ARMENGAUD, J., Benndorf, D., Blakeley-Ruiz, J. A., Brauer, M., Cheng, K., … Initiative, T. M. (2025, May 6). IMETA, Vol. 5.

The case for microbiome stewardship: what it is and how to get there

MSystems.

High-quality draft genome sequences of seven <i>Ralstonia</i> spp. isolated from temperate forest soils

Chan, A. L. H., Choudoir, M. J., Narayanan, A., Rodriguez-Ramos, D., Pold, G., Billings, A. F., & DeAngelis, K. M. (2025, April 14). (S. Roux, Ed.). MICROBIOLOGY RESOURCE ANNOUNCEMENTS, Vol. 4.

Data-Independent Acquisition Mass Spectrometry as a Tool for Metaproteomics: Interlaboratory Comparison Using a Model Microbiome

Rajczewski, A. T., Blakeley-Ruiz, J. A., Meyer, A., Vintila, S., Mcilvin, M. R., Bossche, T., … Jagtap, P. D. (2025, April 10). PROTEOMICS, Vol. 4.

Dietary protein source alters gut microbiota composition and function

ISME JOURNAL, 19(1).

Pangenomes suggest ecological-evolutionary responses to experimental soil warming

Choudoir, M. J., Narayanan, A., Rodriguez-Ramos, D., Simoes, R., Efroni, A., Sondrini, A., & Deangelis, K. M. (2025, March 19). (S. G. Tringe, Ed.). MSPHERE, Vol. 3.

Large Quantities of Bacterial DNA and Protein in Common Dietary Protein Source Used in Microbiome Studies

Bartlett, A., Blakeley-Ruiz, J. A., Richie, T., Theriot, C. M., & Kleiner, M. (2025, February 21). PROTEOMICS, Vol. 2.