Microbiomes and Complex Microbial Communities

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. (2026, January 15). Phytobiomes Journal.

Draft genomes of six Streptomyces species from a United States biogeography survey

Microbiology Resource Announcements.

Investigating the restriction-modification barrier to DNA delivery in human gut probiotic bacteria for streamlined genetic tool development

Advanced Drug Delivery Reviews, 227, 115723.

Targeted DNA ADP-ribosylation triggers templated repair in bacteria and base mutagenesis in eukaryotes

Nature Biotechnology.

Investigating GERMs: How Genotype, Environment, and Rhizosphere Microbiome interactions underlie heat response in maize and sorghum

Korth, N., Borrero, I., Rumley, K., Woodley, A. L., Choudoir, M. J., & Gage, J. L. (2025, December 10).

Toluene-2-monooxygenase expression and trichloroethene oxidizing activity of Burkholderia vietnamiensis G4 grown on benzyl alcohol and benzyl esters

Saito, A. M., Oyarzún, A. P., Hyman, M. R., & Semprini, L. (2025, December 19). Applied Microbiology and Biotechnology.

Evaluation of statistical approaches for differential metaproteomics: Reproducible code

Hinzke, T., Kunath, B. J., Blakeley-Ruiz, J. A., Korenek, A., Vintila, S., Wilmes, P., & Kleiner, M. (2025, December 10). Zenodo (CERN European Organization for Nuclear Research).

Evaluation of statistical approaches for differential metaproteomics: Reproducible code

Hinzke, T., Kunath, B. J., Blakeley-Ruiz, J. A., Korenek, A., Vintila, S., Wilmes, P., & Kleiner, M. (2025, December 10). Zenodo (CERN European Organization for Nuclear Research).

Evaluation of statistical approaches for differential metaproteomics

Hinzke, T., Kunath, B. J., Blakeley-Ruiz, J. A., Korenek, A., Vintila, S., Wilmes, P., & Kleiner, M. (2025, December 10). (Vol. 12). Vol. 12.

Techno-economic analysis of industrial-scale fermentation for formate dehydrogenase (FDH) production

Cunniffe, J., Berrio, V. R., Hunter, C., Nguyen, T., Salmon, S., Crook, N., … Sagues, W. J. (2025, December 6). Bioresources and Bioprocessing.

MassIVE MSV000100012 - Aerobic catabolism of isobutylene by Mycolicibacterium sp. ELW1 requires plasmid-borne ibc genes

Hyman, M. (2025, January 1). UC San Diego.

Successful Fecal Microbiota Transplants in Post-antibiotic Treated Recurrent Clostridioides difficile Patients Induce Acylcarnitine and Sphingolipid Lipidomic Shifts

Gancz, A., Zhang, G., McMillan, A., Dougherty, M., McGill, S., Gulati, A., … Theriot, C. (2025, November 3).

Assessing the diversity and functional profile of the “microbial proteome” in fermented foods

Winkler, L., Awan, A., Rideout, N. M., Kleiner, M., & Rideout, N. (2025, November 19). BioRxiv (Cold Spring Harbor Laboratory).

Structure-guided design of a synthetic bile acid that inhibits Clostridioides difficile TcdB toxin

Miletic, S., Icho, S., Li, Z., Tam, J., Rose, E. C., Perkins, C. E., … Melnyk, R. A. (2025, November 18). Nature Microbiology.

Comparative performance of Scribe and database search engines in metaproteomic profiling of a ground-truth microbiome dataset

Rajczewski, A. T., Mehta, S., Wagner, R., Gabriel, W., Johnson, J., Do, K., … Jagtap, P. D. (2025, October 22). Journal of Proteomics.

Development of Peptide Glucosyltransferase Inhibitors With Comprehensive Coverage Across <i>Clostridioides difficile</i> Toxin B Sub‐Types

Catella, C. M., Sarma, S., Hinesley, C. M., Febo, C. E., Breau, K. A., Durmusoglu, D., … Crook, N. (2025, November 14). Biotechnology and Bioengineering.

Comparative Genomics of the Endosymbiont <i>Cardinium</i> Causing Reproductive Manipulation in <i>Encarsia</i> Parasitoid Wasps

Comparative Genomics of the Endosymbiont Cardinium Causing Reproductive Manipulation in Encarsia Parasitoid Wasps. MicrobiologyOpen.

Diverse bacteriohemerythrin genes of <i>Methylomonas denitrificans</i> FJG1 provide insight into the survival and activity of methanotrophs in low oxygen ecosystems

Weiblen, C., Kits, K. D., Kleiner, M., Sauvageau, D., & Stein, L. Y. (2025, September 25). (C. M. Cavanaugh, Ed.). MBio, Vol. 9.

The emerging roles of non-<i>Saccharomyces</i> yeasts in fermented foods and human health

The emerging roles of non-Saccharomyces yeasts in fermented foods and human health. FEMS Yeast Research.

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 <i>Cardinium</i>: a widespread heritable endosymbiont of invertebrates

Mathieson, O. L., Schultz, D. L., Hunter, M. S., Kleiner, M., Schmitz-Esser, S., & Doremus, M. R. (2025, January 1). FEMS Microbiology Reviews, Vol. 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.