Jitender Yadav, Tao Liang, Tairan Qin, Nayanan Nathan, Katherine J.P. Schwenger, Lauren Pickel, Li Xie, Helena Lei, Daniel A. Winer, Heather Maughan, Susan J. Robertson, Minna Woo, Wendy Lou, Kate Banks, Timothy Jackson, Allan Okrainec, Susy S. Hota, Susan M. Poutanen, Hoon-Ki Sung, Johane P. Allard, Dana J. Philpott, and Herbert Y. Gaisano

Cell Rep Med 2023 May 16;4(5):101051. doi: 10.1016/j.xcrm.2023.101051

Pubmed: 37196633

Abstract

Alterations in the microbiome correlate with improved metabolism in patients following bariatric surgery. While fecal microbiota transplantation (FMT) from obese patients into germ-free (GF) mice has suggested a significant role of the gut microbiome in metabolic improvements following bariatric surgery, causality remains to be confirmed. Here, we perform paired FMT from the same obese patients (BMI > 40; four patients), pre- and 1 or 6 months post-Roux-en-Y gastric bypass (RYGB) surgery, into Western diet-fed GF mice. Mice colonized by FMT from patients’ post-surgery stool exhibit significant changes in microbiota composition and metabolomic profiles and, most importantly, improved insulin sensitivity compared with pre-RYGB FMT mice. Mechanistically, mice harboring the post-RYGB microbiome show increased brown fat mass and activity and exhibit increased energy expenditure. Moreover, improvements in immune homeostasis within the white adipose tissue are also observed. Altogether, these findings point to a direct role for the gut microbiome in mediating improved metabolic health post-RYGB surgery.

Kathryn J. McTavish, Renan N. D. Almeida, Jonathan Tersigni, Melina K. Raimundi, Yunchen Gong, Pauline W. Wang, Guilherme F. Gontijo, Ricardo M. de Souza, Mario L. V. de Resende, Darrell Desveaux, David S. Guttman

New Phytol 2024 Jan;241(1):409-429. doi: 10.1111/nph.19364

Pubmed: 37953378

Abstract

The emergence of new pathogens is an ongoing threat to human health and agriculture. While zoonotic spillovers received considerable attention, the emergence of crop diseases is less well studied. Here, we identify genomic factors associated with the emergence of Pseudomonas syringae bacterial blight of coffee. Fifty-three P. syringae strains from diseased Brazilian coffee plants were sequenced. Comparative and evolutionary analyses were used to identify loci associated with coffee blight. Growth and symptomology assays were performed to validate the findings. Coffee isolates clustered in three lineages, including primary phylogroups PG3 and PG4, and secondary phylogroup PG11. Genome-wide association study of the primary PG strains identified 37 loci, including five effectors, most of which were encoded on a plasmid unique to the PG3 and PG4 coffee strains. Evolutionary analyses support the emergence of coffee blight in PG4 when the coffee-associated plasmid and associated effectors derived from a divergent plasmid carried by strains associated with other hosts. This plasmid was only recently transferred into PG3. Natural diversity and CRISPR-Cas9 plasmid curing were used to show that strains with the coffee-associated plasmid grow to higher densities and cause more severe disease symptoms in coffee. This work identifies possible evolutionary mechanisms underlying the emergence of a new lineage of coffee pathogens.

Lucía Graña-Miraglia, Nadia Morales-Lizcano, Pauline W. Wang, David M. Hwang, Yvonne C. W. Yau, Valerie J. Waters, David S. Guttman

PLoS Comput Biol. 2023 Sep 6;19(9):e1011424. doi: 10.1371/journal.pcbi.1011424

Pubmed: 37672526

Abstract

Chronic Pseudomonas aeruginosa (Pa) lung infections are the leading cause of mortality among cystic fibrosis (CF) patients; therefore, the eradication of new-onset Pa lung infections is an important therapeutic goal that can have long-term health benefits. The use of early antibiotic eradication therapy (AET) has been shown to clear the majority of new-onset Pa infections, and it is hoped that identifying the underlying basis for AET failure will further improve treatment outcomes. Here we generated machine learning models to predict AET outcomes based on pathogen genomic data. We used a nested cross validation design, population structure control, and recursive feature selection to improve model performance and showed that incorporating population structure control was crucial for improving model interpretation and generalizability. Our best model, controlling for population structure and using only 30 recursively selected features, had an area under the curve of 0.87 for a holdout test dataset. The top-ranked features were generally associated with motility, adhesion, and biofilm formation.

Thaïs A. Bernos, Sunčica Avlijaš, Jaclyn Hill, Olivier Morissette, Anthony Ricciardi, Nicholas E. Mandrak, Kenneth M. Jeffries

Evolutionary Applications. 2023. 16 (1) 173-188. doi: 10.1111/eva.13520

Abstract

Introduced and geographically expanding populations experience similar eco-evolutionary challenges, including founder events, genetic bottlenecks, and novel environments. Theory predicts that reduced genetic diversity resulting from such phenomena limits the success of introduced populations. Using 1900 SNPs obtained from restriction-site-associated DNA sequencing, we evaluated hypotheses related to the invasion history and connectivity of an invasive population of Tench (Tinca tinca), a Eurasian freshwater fish that has been expanding geographically in eastern North America for three decades. Consistent with the reported history of a single introduction event, our findings suggest that multiple introductions from distinct genetic sources are unlikely as Tench had a small effective population size (~114 [95% CI = 106–123] individuals), no strong population subdivision across time and space, and evidence of a recent genetic bottleneck. The large genetic neighbourhood size (220 km) and weak within-population genetic substructure suggested high connectivity across the invaded range, despite the relatively large area occupied. There was some evidence for a small decay in genetic diversity as the species expanded northward, but not southward, into new habitats. As eradicating the species within a ~112 km radius would be necessary to prevent recolonization, eradicating Tench is likely not feasible at watershed—and possibly local—scales. Management should instead focus on reducing abundance in priority conservation areas to mitigate adverse impacts. Our study indicates that introduced populations can thrive and exhibit relatively high levels of genetic diversity despite severe bottlenecks (<1.5% of the ancestral effective population size) and suggests that landscape heterogeneity and population demographics can generate variability in spatial patterns of genetic diversity within a single range expansion.

Kavishka S. Gallage, Alexander Van Nynatten, Nathan K. Lujan, Nathan R. Lovejoy, and Nicholas E. Mandrak

Canadian Journal of Fisheries and Aquatic Sciences. 6 September 2023. doi: 10.1139/cjfas-2023-0061

Abstract

Detection of early life stages of fishes is important for understanding life history patterns and critical spawning habitats. When feasible, identifying early life stages of fishes using morphology requires taxonomic expertise and can be challenging, time consuming, and imprecise. In this study, we used DNA metabarcoding to identify egg and larval batch samples from two sites in the species-rich East Sydenham River, Ontario, Canada. We used a two-step PCR metabarcoding approach to amplify a highly variable region of the mitochondrial COI gene from 1075 mixed species batch samples. Amplicon libraries were sequenced with Illumina Mi-seq and the sequencing reads were filtered and assembled using the software package mothur. Barcodes were then classified using a reference library comprised of Great Lakes fishes and potential invaders. In total, 34 species, including three at-risk species and three invasive species, were detected at the two sampling sites. This study shows the potential utility of metabarcoding for detection and identification of early life stage Great Lake fishes.

Alexander Van Nynatten, Kavishka S. Gallage, Nathan K. Lujan, Nicholas E. Mandrak, Nathan R. Lovejoy

Mol Ecol Resour 2023 Aug;23(6):1319-1333 doi: 10.1111/1755-0998

Pubmed ID: 37101312

Abstract

Detection of invasive species is critical for management but is often limited by challenges associated with capture, processing and identification of early life stages. DNA metabarcoding facilitates large-scale monitoring projects to detect establishment early. Here, we test the use of DNA metabarcoding to monitor invasive species by sequencing over 5000 fishes in bulk ichthyoplankton samples (larvae and eggs) from four rivers of ecological and cultural importance in southern Canada. We were successful in detecting species known from each river and three invasive species in two of the four rivers. This includes the first detection of early life-stage rudd in the Credit River. We evaluated whether sampling gear affected the detection of invasive species and estimates of species richness, and found that light traps outperform bongo nets in both cases. We also found that the primers used for the amplification of target sequences and the number of sequencing reads generated per sample affect the consistency of species detections. However, these factors have less impact on detections and species richness estimates than the number of samples collected and analysed. Our analyses also show that incomplete reference databases can result in incorrectly attributing DNA sequences to invasive species. Overall, we conclude that DNA metabarcoding is an efficient tool for monitoring the early establishment of invasive species by detecting evidence of reproduction but requires careful consideration of sampling design and the primers used to amplify, sequence and classify the diversity of native and potentially invasive species.

Connor R. Fitzpatrick, Julia Copeland, Pauline W. Wang, David S. Guttman, Peter M. Kotanen, Marc T. J. Johnson

Mol Plant Microbe Interact 2023 Mar;36(3):165-175. doi: 10.1094/MPMI-09-22-0188-R.

PMID: 36463399

Abstract

The root microbiome is composed of distinct epiphytic (rhizosphere) and endophytic (endosphere) habitats. Differences in abiotic and biotic factors drive differences in microbial community diversity and composition between these habitats, though how they shape the interactions among community members is unknown. Here, we coupled a large-scale characterization of the rhizosphere and endosphere bacterial communities of 30 plant species across two watering treatments with co-occurrence network analysis to understand how root habitats and soil moisture shape root bacterial network properties. We used a novel bootstrapping procedure and null network modeling to overcome some of the limitations associated with microbial co-occurrence network construction and analysis. Endosphere networks had elevated node betweenness centrality versus the rhizosphere, indicating greater overall connectivity among core bacterial members of the root endosphere. Taxonomic assortativity was higher in the endosphere, whereby positive co-occurrence was more likely between bacteria within the same phylum while negative co-occurrence was more likely between bacterial taxa from different phyla. This taxonomic assortativity could be driven by positive and negative interactions among members of the same or different phylum, respectively, or by similar niche preferences associated with phylum rank among root inhabiting bacteria across plant host species. In contrast to the large differences between root habitats, drought had limited effects on network properties but did result in a higher proportion of shared co-occurrences between rhizosphere and endosphere networks. Our study points to fundamentally different ecological processes shaping bacterial co-occurrence across root habitats.

Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Michael Fralick, Caroline Nott, Jason Moggridge, Lucas Castellani, Ashley Raudanskis, David S. Guttman, Aaron Hinz, Nisha Thampi, Alex Wong, Doug Manuel, Allison McGeer, Evgueni Doukhanine, Hebah Mejbel, Veronica Zanichelli, Madison Burella, Sylva L. Donaldson, Pauline W. Wang, Rees Kassen, Derek R. MacFadden

NEJM Evid 2023;2(3) doi: 10.1056/EVIDoa2200203

Pubmed: 38320044

Abstract

Background

Environmental surveillance of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) through wastewater has become a useful tool for population-level surveillance. Built environment sampling may provide a more spatially refined approach for surveillance in congregate living settings.

Methods

We conducted a prospective study in 10 long-term care homes (LTCHs) between September 2021 and November 2022. Floor surfaces were sampled weekly at multiple locations within each building and analyzed for the presence of SARS-CoV-2 using quantitative reverse transcriptase polymerase chain reaction. The primary outcome was the presence of a coronavirus disease 2019 (Covid-19) outbreak in the week that floor sampling was performed.

Results

Over the 14-month study period, we collected 4895 swabs at 10 LTCHs. During the study period, 23 Covid-19 outbreaks occurred with 119 cumulative weeks under outbreak. During outbreak periods, the proportion of floor swabs that were positive for SARS-CoV-2 was 54.3% (95% confidence interval [CI], 52 to 56.6), and during non-outbreak periods it was 22.3% (95% CI, 20.9 to 23.8). Using the proportion of floor swabs positive for SARS-CoV-2 to predict Covid-19 outbreak status in a given week, the area under the receiver-operating characteristic curve was 0.84 (95% CI, 0.78 to 0.9). Among 10 LTCHs with an outbreak and swabs performed in the prior week, eight had positive floor swabs exceeding 10% at least 5 days before outbreak identification. For seven of these eight LTCHs, positivity of floor swabs exceeded 10% more than 10 days before the outbreak was identified.

Conclusions

Detection of SARS-CoV-2 on floors is strongly associated with Covid-19 outbreaks in LTCHs. These data suggest a potential role for floor sampling in improving early outbreak identification.

Stephanie Tan, Kelvin Cho, Justin R. Nodwell

J Biol Chem 2022 Oct;298(10):102473. doi: 10.1016/j.jbc.2022.102473.

PMID: 36089064

Abstract

WalKR is a two-component system that is essential for viability in Gram-positive bacteria that regulates the all-important autolysins in cell wall homeostasis. Further investigation of this essential system is important for identifying ways to address antibiotic resistance. Here, we show that a T101M mutation in walR confers a defect in autolysis, a thickened cell wall, and decreased susceptibility to antibiotics that target lipid II cycle, a phenotype that is reminiscent of the clinical resistance form known as vancomycin intermediate-resistant Staphylococcus aureus. Importantly, this is accompanied by dramatic sensitization to tunicamycin. We demonstrate that this phenotype is due to partial collapse of a pathway consisting of autolysins, AtlA and Sle1, a transmembrane sugar permease, MurP, and GlcNAc recycling enzymes, MupG and MurQ. We suggest that this causes a shortage of substrate for the peptidoglycan biosynthesis enzyme MraY, causing it to be hypersensitive to competitive inhibition by tunicamycin. In conclusion, our results constitute a new molecular model for antibiotic sensitivity in S. aureus and a promising new route for antibiotic discovery.

Arjan Banerjee, Sasa Stefanovic

Planta 2023 Feb 24;257(4):66. doi: 10.1007/s00425-023-04099-y.

PMID: 36826697

Abstract

Most species in Cuscuta subgenus Grammica retain many photosynthesis-related plastid genes, generally under purifying selection. A group of holoparasitic species in section Subulatae may have lost their plastid genomes entirely. The c. 153 species of plants belonging to Cuscuta subgenus Grammica are all obligate stem parasites. However, some have completely lost the ability to conduct photosynthesis while others retain photosynthetic machinery and genes. The plastid genome that primarily encodes key photosynthesis genes functions as a bellwether for how reliant plants are on primary production. This research assembles and analyses 17 plastomes across Cuscuta subgenus Grammica with the aim of characterizing the state of the plastome in each of its sections. By comparing the structure and content of plastid genomes across the subgenus, as well as by quantifying the selection acting upon each gene, we reconstructed the patterns of plastome change within the phylogenetic context for this group. We found that species in 13 of the 15 sections that comprise Grammica retain the bulk of plastid photosynthesis genes and are thus hemiparasitic. The complete loss of photosynthesis can be traced to two clades: the entire section Subulatae and a complex of three species within section Ceratophorae. We were unable to recover any significant plastome sequences from section Subulatae, suggesting that plastomes in these species are either drastically reduced or lost entirely.