Category: Publications

Amandeep Kaur, Jeffrey B Jones, Erica M Goss, Yesim Aysan, Marcus M Dillon

Access Microbiol. 2026 Feb 27;8(2):001144.v3. doi: 10.1099/acmi.0.001144.v3.

Pubmed: 41767906

Abstract

Xanthomonas spp. are increasingly recognized as a global threat to agriculture, impacting a broad range of economically important crops. We report the whole-genome sequences of six Xanthomonas strains isolated from tomato and pepper plants in Turkey that were experiencing symptoms of bacterial spot disease. Phylogenomic analysis with representative Xanthomonas genomes from each species revealed that three of these strains belonged to Xanthomonas perforans, two to Xanthomonas euvesicatoria and one to Xanthomonas campestris. We then analysed the phylogenomic relatedness of these strains with other strains from these respective species and characterized their type III secreted effector content. These genomic data represent a valuable resource for understanding the genetic diversity and local epidemiology of bacterial spot disease in Turkey.

Keywords: Xanthomonas; bacterial spot disease; phylogenomics; type III secretion effectors; whole-genome sequencing.

Sara Shama, Michelle R Asbury, Alex Kiss , Nicole Bando , James Butcher, Elena M Comelli, Julia K Copeland , Adrianna Greco , Akash Kothari , Philip M Sherman, Alain Stintzi , Amel Taibi, Christopher Tomlinson, Sharon Unger , Pauline W Wang ; OptiMoM Feeding Group; Deborah L O’Connor

Cell Rep Med. 2024 Sep 17;5(9):101729. doi: 10.1016/j.xcrm.2024.101729.

Pubmed: 39243753

Abstract

Mother’s milk contains diverse bacterial communities, although their impact on microbial colonization in very-low-birth-weight (VLBW, <1,500 g) infants remains unknown. Here, we examine relationships between the microbiota in preterm mother’s milk and the VLBW infant gut across initial hospitalization (n = 94 mother-infant dyads, 422 milk-stool pairs). Shared zero-radius operational taxonomic units (zOTUs) between milk-stool pairs account for ∼30%-40% of zOTUs in the VLBW infant’s gut. We show dose-response relationships between intakes of several genera from milk and their concentrations in the infant’s gut. These relationships and those related to microbial sharing change temporally and are modified by in-hospital feeding practices (especially direct breastfeeding) and maternal-infant antibiotic use. Correlations also exist between milk and stool microbial consortia, suggesting that multiple milk microbes may influence overall gut communities together. These results highlight that the mother’s milk microbiota may shape the gut colonization of VLBW infants by delivering specific bacteria and through intricate microbial interactions.

Trial registration: ClinicalTrials.gov NCT02137473.

Keywords: antibiotics; direct breastfeeding; donor milk; human milk; microbiome; microbiota; mother’s milk; nutrient fortification; preterm infant; very-low-birth-weight infant.

Anna van Weringh, Paul J Gamueda, Hasna Khan, Asher Pasha, Eddi Esteban, Nicholas J Provart

Plant Cell. 2025 Oct 8;37(10):koaf218. doi: 10.1093/plcell/koaf218.

Pubmed: 40973624

Abstract

Drought is an important environmental stress that limits crop production. Guard cells (GCs) act to control the rate of water loss. To better understand how gene expression in GCs changes during progressive drought, we generated GC-specific RNA-seq transcriptomes during mild, moderate, and severe drought stress. Additionally, we sampled re-watered plants after severe drought. These transcriptomes were generated using the INTACT (isolation of nuclei tagged in specific cell types) system to capture the RNA from GC nuclei. We optimized the INTACT protocol for Arabidopsis thaliana leaf tissue, incorporating fixation to preserve RNA during nuclear isolation. To identify gene expression changes unique to GCs, we also generated INTACT transcriptomes from all leaf cell types, using the 35S viral promoter. These data sets highlight shared and unique gene expression changes between GCs and the bulk leaf tissue. Only GCs have detectable gene expression changes at the earliest drought time point, and a high percentage of moderate drought GC DEGs are not observed in severe drought, unlike the bulk leaf tissue, showing that GCs tailor their gene expression changes to drought severity. A thermal imaging screen of mutants of 80 candidate early drought-responsive genes revealed that 10 of these exhibit a cooler-than-wild-type phenotype under moderate drought conditions. The drought-responsive GC and leaf RNA-seq transcriptomes are available in the Arabidopsis ePlant at the Bio-Analytic Resource for Plant Biology website. These findings provide valuable insights into GC-specific drought responses and identify targets for enhancing drought tolerance in crops.

Zachary Kileeg, G Adam Mott

BMC Biol. 2025 Aug 26;23(1):266. doi: 10.1186/s12915-025-02364-y

Pubmed: 40859252

Abstract

Background: The receptor-like kinases (RLKs) are the largest family of proteins in plants. Characterized members play critical roles in diverse processes from growth to immunity, and yet the majority do not have a known function. Assigning function to RLKs poses a significant challenge due to the specificity of ligand recognition and because of the often pleiotropic or redundant functions RLKs possess. These problems inhibit the important work of identifying stress-related receptors that may be targets for crop improvement. Identification of stress-related evolutionary signatures can provide a way to expedite the discovery of candidate receptors. Pan-genome analysis can be used to compare naturally occurring variants within a species to identify evolutionary signatures that may otherwise be hidden by using only a single ecotype.

Results: Using 146 ecotypes of Arabidopsis, we generated a pan-RLKome to investigate species-wide natural diversity and identify structural variation and other patterns indicative of stress adaptation. We discovered significant presence/absence variation across a subset of RLKs, most of which occurred in specific subclades nested within receptor subfamilies. These same subclades tended to have arisen through proximal or tandem duplication, both of which are common mechanisms during the expansion of stress-related genes. We also identified strong positive selection across many gene subfamilies and a bias of positive selection in the extracellular domains of receptors. This suggests escape from adaptive conflict within the extracellular domain may have played a large role in the evolution and adaptation of the RLKs.

Conclusion: Taken together, this work represents an excellent tool for the comparative study of RLKs and has identified lineages and subclades within RLK subfamilies with the hallmarks of involvement in stress adaptation.

Keywords: PTI; Pan-RLKome; Plant immunity; RLK evolution; RLKs.

Gianni M Castiglione , Yan L I Chiu , Eduardo de A Gutierrez , Alexander Van Nynatten , Frances E Hauser , Matthew Preston , Nihar Bhattacharyya , Ryan K Schott , Belinda S W Chang

Curr Biol. 2023 Nov 6;33(21):4733-4740.e4. doi: 10.1016/j.cub.2023.09.015

Pubmed: 37776863

Abstract

Animals with enhanced dim-light sensitivity are at higher risk of light-induced retinal degeneration when exposed to bright light conditions.^1,2,3,4 This trade-off is mediated by the rod photoreceptor sensory protein, rhodopsin (RHO), and its toxic vitamin A chromophore by-product, all-trans retinal.^5,6,7,8 Rod arrestin (Arr-1) binds to RHO and promotes sequestration of excess all-trans retinal,^9,10 which has recently been suggested as a protective mechanism against photoreceptor cell death.^2,11 We investigated Arr-1 evolution in animals at high risk of retinal damage due to periodic bright-light exposure of rod-dominated retinas. Here, we find the convergent evolution of enhanced Arr-1/RHO all-trans-retinal sequestration in owls and deep-diving whales. Statistical analyses reveal a parallel acceleration of Arr-1 evolutionary rates in these lineages, which is associated with the introduction of a rare Arr-1 mutation (Q69R) into the RHO-Arr-1 binding interface. Using in vitro assays, we find that this single mutation significantly enhances RHO-all-trans-retinal sequestration by ∼30%. This functional convergence across 300 million years of evolutionary divergence suggests that Arr-1 and RHO may play an underappreciated role in the photoprotection of the eye, with potentially vast clinical significance.

Keywords: Stargardt; age-related macular degeneration; all trans retinal; arrestin; blindness; evolution; owl; rhodopsin; vision; whale.

Castiglione GM, Hauser FE, Van Nynatten A, Chang BSW.

Mol Biol Evol. 2023 Apr 4;40(4):msad030. doi: 10.1093/molbev/msad030.

Pubmed: 36763103

Abstract

Extreme environments, such as Antarctic habitats, present major challenges for many biological processes. Antarctic icefishes (Crynotothenioidea) represent a compelling system to investigate the molecular basis of adaptation to cold temperatures. Here, we explore how the sub-zero habitats of Antarctic icefishes have impacted rhodopsin (RH1) function, the temperature-sensitive dim-light visual pigment found in rod photoreceptors. Using likelihood models and ancestral reconstruction, we find that accelerated evolutionary rates in icefish RH1 underlie unique amino acid mutations absent from other deep-dwelling fishes, introduced before (S160A) and during (V259M) the onset of modern polar conditions. Functional assays reveal that these mutations red-shift rhodopsin spectral absorbance, consistent with spectral irradiance under sea ice. These mutations also lower the activation energy associated with retinal release of the light-activated RH1, and accelerate its return to the dark state, likely compensating for a cold-induced decrease in kinetic rates. These are adaptations in key properties of rhodopsin that mediate rod sensitivity and visual performance in the cold dark seas of the Antarctic.

Keywords: icefish; rhodopsin; vision.

Raygoza Garay JA, Turpin W, Lee SH, Smith MI, Goethel A, Griffiths AM, Moayyedi P, Espin-Garcia O, Abreu M, Aumais GL, Bernstein CN, Biron IA, Cino M, Deslandres C, Dotan I, El-Matary W, Feagan B, Guttman DS, Huynh H, Dieleman LA, Hyams JS, Jacobson K, Mack D, Marshall JK, Otley A, Panaccione R, Ropeleski M, Silverberg MS, Steinhart AH, Turner D, Yerushalmi B, Paterson AD, Xu W; CCC GEM Project Research Consortium; Croitoru K.

Gastroenterology. 2023 Sep;165(3):670-681. doi: 10.1053/j.gastro.2023.05.032

Pubmed: 37263307

Abstract

Background & aims: The cause of Crohn’s disease (CD) is unknown, but the current hypothesis is that microbial or environmental factors induce gut inflammation in genetically susceptible individuals, leading to chronic intestinal inflammation. Case-control studies of patients with CD have cataloged alterations in the gut microbiome composition; however, these studies fail to distinguish whether the altered gut microbiome composition is associated with initiation of CD or is the result of inflammation or drug treatment.

Methods: In this prospective cohort study, 3483 healthy first-degree relatives (FDRs) of patients with CD were recruited to identify the gut microbiome composition that precedes the onset of CD and to what extent this composition predicts the risk of developing CD. We applied a machine learning approach to the analysis of the gut microbiome composition (based on 16S ribosomal RNA sequencing) to define a microbial signature that associates with future development of CD. The performance of the model was assessed in an independent validation cohort.

Results: In the validation cohort, the microbiome risk score (MRS) model yielded a hazard ratio of 2.24 (95% confidence interval, 1.03-4.84; P = .04), using the median of the MRS from the discovery cohort as the threshold. The MRS demonstrated a temporal validity by capturing individuals that developed CD up to 5 years before disease onset (area under the curve > 0.65). The 5 most important taxa contributing to the MRS included Ruminococcus torques, Blautia, Colidextribacter, an uncultured genus-level group from Oscillospiraceae, and Roseburia.

Conclusion: This study is the first to demonstrate that gut microbiome composition is associated with future onset of CD and suggests that gut microbiome is a contributor in the pathogenesis of CD.

Keywords: Faecalibacterium; Fecal Calprotectin; Microbiome; Preclinical Inflammatory Bowel Disease; Vitamins B.

Vincent Lau & Nicholas J. Provart

Methods Mol Biol. 2023:2698:351-360. doi: 10.1007/978-1-0716-3354-0_20

Pubmed: 37682484

Abstract

Gene regulatory networks (GRNs) are important for determining how an organism develops and how it responds to external stimuli. In the case of Arabidopsis thaliana, several GRNs have been identified covering many important biological processes. We present AGENT, the Arabidopsis GEne Network Tool, for exploring and analyzing published GRNs. Using tools in AGENT, regulatory motifs such as feed-forward loops can be easily identified. Nodes with high centrality-and hence importance-can likewise be identified. Gene expression data can also be overlaid onto GRNs to help discover subnetworks acting in specific tissues or under certain conditions.

Keywords: Bioinformatics; Feed-forward loops; Gene regulatory networks; Hypothesis generation; Motifs; Protein–DNA interactions; Protein–protein interactions.

Ashley M. Rooney , Kyla Cochrane, Stephanie Fedsin, Samantha Yao, Shaista Anwer, Satyender Dehmiwal, Susy Hota, Susan Poutanen, Emma Allen-Vercoe , Bryan Coburn , MTOP Investigators

mBio. 2023 Aug 31;14(4):e0348222. doi: 10.1128/mbio.03482-22

Pubmed: 37404011

Abstract

Intestinal colonization with pathogens and antimicrobial-resistant organisms (AROs) is associated with increased risk of infection. Fecal microbiota transplant (FMT) has successfully been used to cure recurrent Clostridioides difficile infection (rCDI) and to decolonize intestinal AROs. However, FMT has significant practical barriers to safe and broad implementation. Microbial consortia represent a novel strategy for ARO and pathogen decolonization, with practical and safety advantages over FMT. We undertook an investigator-initiated analysis of stool samples collected from previous interventional studies of a microbial consortium, microbial ecosystem therapeutic (MET-2), and FMT for rCDI before and after treatment. Our aim was to assess whether MET-2 was associated with decreased Pseudomonadota (Proteobacteria) and antimicrobial resistance gene (ARG) burden with similar effects to FMT. Participants were selected for inclusion if baseline stool had Pseudomonadota relative abundance ≥10%. Pre- and post-treatment Pseudomonadota relative abundance, total ARGs, and obligate anaerobe and butyrate-producer relative abundances were determined by shotgun metagenomic sequencing. MET-2 administration had similar effects to FMT on microbiome outcomes. The median Pseudomonadota relative abundance decreased by four logs after MET-2 treatment, a greater decrease than that observed after FMT. Total ARGs decreased, while beneficial obligate anaerobe and butyrate-producer relative abundances increased. The observed microbiome response remained stable over 4 months post-administration for all outcomes. IMPORTANCE Overgrowth of intestinal pathogens and AROs is associated with increased risk of infection. With the rise in antimicrobial resistance, new therapeutic strategies that decrease pathogen and ARO colonization in the gut are needed. We evaluated whether a microbial consortium had similar effects to FMT on Pseudomonadota abundances and ARGs as well as obligate anaerobes and beneficial butyrate producers in individuals with high Pseudomonadota relative abundance at baseline. This study provides support for a randomized, controlled clinical trial of microbial consortia (such as MET-2) for ARO decolonization and anaerobe repletion.

Keywords: Proteobacteria; Pseudomonadota; anaerobes; antibiotic resistance; fecal microbiota transplant; gut microbiome; microbial consortium.

Katherine J. P. Schwenger, Divya Sharma, Yasaman Ghorbani, Wei Xu, Wendy Lou, Elena M. Comelli, Sandra E. Fischer, Timothy D. Jackson, Allan Okrainec, Johane P. Allard

Liver Int. 2024 Feb 14. doi: 10.1111/liv.15864 doi: 10.1111/liv.15864

Pubmed: 38353022

Abstract

Background and aims: Bacterial species and microbial pathways along with metabolites and clinical parameters may interact to contribute to non-alcoholic fatty liver disease (NAFLD) and disease severity. We used integrated machine learning models and a cross-validation approach to assess this interaction in bariatric patients.

Methods: 113 patients undergoing bariatric surgery had clinical and biochemical parameters, blood and stool metabolite measurements as well as faecal shotgun metagenome sequencing to profile the intestinal microbiome. Liver histology was classified as normal liver obese (NLO; n = 30), simple steatosis (SS; n = 41) or non-alcoholic steatohepatitis (NASH; n = 42); fibrosis was graded F0 to F4.

Results: We found that those with NASH versus NLO had an increase in potentially harmful E. coli, a reduction of potentially beneficial Alistipes putredinis and an increase in ALT and AST. There was higher serum glucose, faecal 3-(3-hydroxyphenyl)-3-hydroxypropionic acid and faecal cholic acid and lower serum glycerophospholipids. In NAFLD, those with severe fibrosis (F3-F4) versus F0 had lower abundance of anti-inflammatory species (Eubacterium ventriosum, Alistipes finegoldii and Bacteroides dorei) and higher AST, serum glucose, faecal acylcarnitines, serum isoleucine and homocysteine as well as lower serum glycerophospholipids. Pathways involved with amino acid biosynthesis and degradation were significantly more represented in those with NASH compared to NLO, with severe fibrosis having an overall stronger significant association with Superpathway of menaquinol-10 biosynthesis and Peptidoglycan biosynthesis IV.

Conclusions: In bariatric patients, NASH and severe fibrosis were associated with specific bacterial species, metabolic pathways and metabolites that may contribute to NAFLD pathogenesis and disease severity.

Keywords: fatty liver; hepatic fibrosis; metabolic pathways; metagenome; morbid obesity.