Microbiomes and Complex Microbial Communities

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

Kleiner, M., Mordant, A., & Blakeley-Ruiz, J. A. (2025, June 23).

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.

Construction of a Heterologous Pathway inEscherichia colifor Terephthalate Assimilation

Li, T., & Crook, N. (2025, February 28).

Pickering Emulsion for Enhanced Viability of Plant Growth Promoting Bacteria and Combined Delivery of Agrochemicals and Biologics

Advanced Functional Materials, 2.

Long-term climate establishes functional legacies by altering microbial traits

ISME JOURNAL, 19(1).

Tree Species Controls Over Nitrogen and Phosphorus Cycling in a Wet Tropical Forest

The Bulletin of the Ecological Society of America.

Source of dietary protein alters the abundance of proteases, intestinal epithelial and immune proteins both directly and via interactions with the gut microbiota

Awan, A., Bartlett, A., Blakeley-Ruiz, J. A., Richie, T., Ziegler, A., & Kleiner, M. (2025, January 9).

Meta-omics reveals role of photosynthesis in microbially induced carbonate precipitation at a CO₂-rich geyser

ISME COMMUNICATIONS, 4(1).

Invasive Buffelgrass, <i>Cenchrus ciliaris</i>, Balances Opportunistic Acquisition of Foliar fungi With Host and Environmental Filtering in Its Introduced Range

Bowman, E. A., Hawkes, C. V., Jones, N., Plowes, R. M., Martin, D. J., & Gilbert, L. E. (2024, December 12). MOLECULAR ECOLOGY, Vol. 12.

Tree species controls over nitrogen and phosphorus cycling in a wet tropical forest

Russell, A. E., Hall, S. J., Bedoya, R., Kivlin, S. N., & Hawkes, C. V. (2024, December 3). ECOLOGICAL MONOGRAPHS, Vol. 12.

A pilot study of metaproteomics and DNA metabarcoding as tools to assess dietary intake in humans

Petrone, B. L., Bartlett, A., Jiang, S., Korenek, A., Vintila, S., Tenekjian, C., … Kleiner, M. (2024, December 12). FOOD & FUNCTION, Vol. 12.

Stable isotope fingerprinting can directly link intestinal microorganisms with their carbon source and captures diet-induced substrate switchingin vivo

Mordant, A., Blakeley-Ruiz, J. A., & Kleiner, M. (2024, December 11).

Genomic and proteomic characterization of sulfate-reducing symbionts of gutless marine annelids

Grace, D. A., Kleiner, M., Mankowski, A., Cifuentes-Anticevic, J., Violette, M. J., Anda, V. D., … Liebeke, M. (2024, December 9).

An intranuclear bacterial parasite of deep-sea mussels expresses apoptosis inhibitors acquired from its host

NATURE MICROBIOLOGY, 9(11).

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

Cortés-Martín, A., Buttimer, C., Maier, J. L., Tobin, C. A., Draper, L. A., Ross, R. P., … Shkoporov, A. N. (2024, November 17).

The biochemical mechanisms of plastic biodegradation

[Review of ]. FEMS MICROBIOLOGY REVIEWS, 48(6).

Community standards and future opportunities for synthetic communities in plant-microbiota research

[Review of ]. NATURE MICROBIOLOGY, 9(11), 2774–2784.

Seasonal effects of long-term warming on ecosystem function and bacterial diversity

PLOS ONE, 19(10).

Metagenomic, metabolomic, and lipidomic shifts associated with fecal microbiota transplantation for recurrent <i>Clostridioides difficile</i> infection

McMillan, A. S., Zhang, G., Dougherty, M. K., McGill, S. K., Gulati, A. S., Baker, E. S., & Theriot, C. M. (2024, October 8). MSPHERE.

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. V. D., … Jagtap, P. D. (2024, September 22).