Regina Lamendella

In this study, we investigated complicated diverticulitis, an inflammatory condition associated with abscesses, fistulas, intestinal obstructions, perforations, and primarily affects adults over the age of 60. Although the exact etiology remains unclear, the gut microbiome has been suggested as a contributing factor. Previous studies have used 16S rRNA gene analysis from patient fecal samples, which is limited to identifying the bacterial communities present. Herein, we employed shotgun metatranscriptomics on 40 patient-matched samples of diseased and adjacent normal colonic mucosal tissues from 20 patients with complicated diverticulitis to gain a more comprehensive understanding of active microbial taxa and gene expression patterns that may be involved in this disease state. Our findings revealed distinct beta diversity and a conglomerate of pathogenic microbiota in the diseased tissues, including Staphylococcus cohnii, Corynebacterium jeikeium, Kineococcus, Talaromyces rugulosus, Campylobacteraceae, and Ottowia, among others. The adjacent normal tissues were a stark contrast, harboring anti-inflammatory taxa such as Streptococcus salivarius and housekeeping genes and pathways such as the ABC-2 type transport system ATP-binding protein. These results align with previous amplicon sequencing studies and provide novel functional insights that may be crucial for understanding the etiology of complicated diverticulitis. IMPORTANCE: Complicated diverticulitis is a virulent condition with no clear cause other than the association with colonic diverticulosis. We assessed the microbial gene expression in complicated diverticulitis patients using colonic tissue samples, revealing microbes in the diseased tissue known to exacerbate the diverticular condition and to live in extreme places, and microbes in patients’ normal tissue known to maintain normal bodily functions. This functional information is therefore important for understanding what microbial taxa are present and what they are doing. It is possible clinicians could someday harness this information to more effectively treat complicated diverticulitis symptoms. For example, clinicians may suggest dietary changes and prescribe probiotics to increase beneficial bacteria. Clinicians may also prescribe targeted antibiotics or consider the emerging treatment option of fecal transplants in complicated diverticulitis patients. While not curing complicated diverticulitis, each potential treatment option mentioned addresses balancing out dysbiosis of the gut microbiome, therefore alleviating associated symptoms.

This study examines the gut microbiome from fecal samples of a reptilian model (Sceloporus undulatus). Vertebrates display a diverse range of variability in gut microbiota. The dynamic host-symbiote interactions between gut microbiota are essential in various metabolic processes and overall health of the host organism. We used 16S rRNA gene sequencing to profile the bacterial community from the guts of wild Eastern Fence Lizards. Microbiome profiles were collected at four distinct time points when lizards were actively foraging in the environment and across four age groups, aiming to characterize the natural variation in bacterial diversity among wild specimens. Bioinformatic analysis was conducted using QIIME2/DADA2 pipelines. Successional changes in the gut microbiome of lizards from the juvenile stage to adulthood revealed a pattern of increased functionality and diversity. Environmental bacteria such as Mycobacterium and Pantoea in young of year (YOY) lizards underwent successional microbiome changes to taxa including Caproiciproducens, Eubacterium, Fusobacterium, and Roseburia in adults, reflecting dietary shifts from maternal nutrients and early-stage prey to fiber-rich arthropod diets. Juvenile lizards exhibited a simple gut microbiome dominated by pioneer colonizers (Firmicutes, Bacteroidota, and Proteobacteria), with alpha diversity increasing rapidly within a month to near adult-levels. This research extends our understanding of reptilian microbiomes, capturing a snapshot of the ecological complexities of Eastern Fence Lizard microbiomes.

The environmental implications of unconventional oil and gas extraction are only recently starting to be systematically recorded. Our research shows the utility of microbial communities paired with geochemical markers to build strong predictive random forest models of unconventional oil and gas activity and the identification of key biomarkers.

We report a draft genome sequence for Streptomyces albidoflavus strain 09MW18-IS, isolated from the Atlantic slope off the coast of Virginia. The whole-genome sequence will provide novel insights into biosynthetic gene clusters and ecological adaptation in an oligotrophic environment.

Hospital-acquired infections (HAIs) pose a serious threat to patients, and hospitals spend billions of dollars each year to reduce and treat these infections. Many HAIs are due to contamination from workers’ hands and contact with high-touch surfaces. Therefore, we set out to test the efficacy of a new preventative technology, AIONX^®Antimicrobial Technologies, Inc’s cleanSURFACES^®, which is designed to complement daily chemical cleaning events by continuously preventing re-colonization of surfaces. To that end, we swabbed surfaces before (Baseline) and after (Post) application of the cleanSURFACES^®at various time points (Day 1, Day 7, Day 14, and Day 28). To circumvent limitations associated with culture-based and 16S rRNA gene amplicon sequencing methodologies, these surface swabs were processed using metatranscriptomic (RNA) analysis to allow for comprehensive taxonomic resolution and the detection of active microorganisms. Overall, there was a significant (P < 0.05) global reduction of microbial diversity in Post-intervention samples. Additionally, Post sample microbial communities clustered together much more closely than Baseline samples based on pairwise distances calculated with the weighted Jaccard distance metric, suggesting a defined shift after product application. This shift was characterized by a general depletion of several microbes among Post samples, with multiple phyla also being reduced over the duration of the study. Notably, specific clinically relevant microbes, includingStaphylococcus aureus,Clostridioides difficileandStreptococcusspp., were depleted Post-intervention. Taken together, these findings suggest that chemical cleaning events used jointly with cleanSURFACES^®have the potential to reduce colonization of surfaces by a wide variety of microbes, including many clinically relevant pathogens.

Summary: Infants are at a high risk of acquiring infections caused by antibiotic resistant bacterial strains. Antibiotic resistance gene (ARG) load is typically higher in newborns than in adults, but it is unknown which factors besides antibiotic treatment affect the load. Our study demonstrates that inclusion of any formula in the newborn diet causes shifts in microbial community composition that result in higher ARG loads in formula-fed infants compared to infants not fed formula. The effect of formula was especially strong in premature newborns and newborns treated with antibiotics. Interestingly, antibiotics alone without formula did not have a detectable impact on the ARG load of the newborn gut. We also observed that formula-fed infants had enriched numbers of pathogenic species and were depleted in typical infant gut species such as Bifidobacterium bifidum . The results suggest infant feeding choices should include assessment of risks associated with elevated ARG abundance.