Enteric pathogens cause widespread foodborne illness and are increasingly resistant to important antibiotics yet their ecological impact on the gut microbiome and resistome is not fully understood. ...Herein, shotgun metagenome sequencing was applied to stool DNA from 60 patients (cases) during an enteric bacterial infection and after recovery (follow-ups). Overall, the case samples harbored more antimicrobial resistance genes (ARGs) with greater resistome diversity than the follow-up samples (p < 0.001), while follow-ups had more diverse gut microbiota (p < 0.001). Although cases were primarily defined by genera Escherichia, Salmonella, and Shigella along with ARGs for multi-compound and multidrug resistance, follow-ups had a greater abundance of Bacteroidetes and Firmicutes phyla and resistance genes for tetracyclines, macrolides, lincosamides, and streptogramins, and aminoglycosides. A host-tracking analysis revealed that Escherichia was the primary bacterial host of ARGs in both cases and follow-ups, with a greater abundance occurring during infection. Eleven distinct extended spectrum beta-lactamase (ESBL) genes were identified during infection, with some detectable upon recovery, highlighting the potential for gene transfer within the community. Because of the increasing incidence of disease caused by foodborne pathogens and their role in harboring and transferring resistance determinants, this study enhances our understanding of how enteric infections impact human gut ecology.
Endophytes often have dramatic effects on their host plants. Characterizing the relationships among members of these communities has focused on identifying the effects of single microbes on their ...host, but has generally overlooked interactions among the myriad microbes in natural communities as well as potential higher-order interactions. Network analyses offer a powerful means for characterizing patterns of interaction among microbial members of the phytobiome that may be crucial to mediating its assembly and function. We sampled twelve endophytic communities, comparing patterns of niche overlap between coexisting bacteria and fungi to evaluate the effect of nutrient supplementation on local and global competitive network structure. We found that, despite differences in the degree distribution, there were few significant differences in the global network structure of niche-overlap networks following persistent nutrient amendment. Likewise, we found idiosyncratic and weak evidence for higher-order interactions regardless of nutrient treatment. This work provides a first-time characterization of niche-overlap network structure in endophytic communities and serves as a framework for higher-resolution analyses of microbial interaction networks as a consequence and a cause of ecological variation in microbiome function.
While enteric pathogens have been widely studied for their roles in causing foodborne infection, their impacts on the gut microbial community have yet to be fully characterized. Previous work has ...identified notable changes in the gut microbiome related to pathogen invasion, both taxonomically and genetically. Characterization of the metabolic landscape during and after enteric infection, however, has not been explored. Consequently, we investigated the metabolome of paired stools recovered from 60 patients (cases) during and after recovery from enteric bacterial infections (follow-ups). Shotgun metagenomics was applied to predict functional microbial pathways combined with untargeted metametabolomics classified by Liquid Chromatography Mass Spectrometry. Notably, cases had a greater overall metabolic capacity with significantly higher pathway richness and evenness relative to the follow-ups (p<0.05). Metabolic pathways related to central carbon metabolism, amino acid metabolism, and lipid and fatty acid biosynthesis were more highly represented in cases and distinct signatures for menaquinone production were detected. By contrast, the follow-up samples had a more diverse metabolic landscape with enhanced richness of polar metabolites (p<0.0001) and significantly greater richness, evenness, and overall diversity of nonpolar metabolites (p<0.0001). Although many metabolites could not be annotated with existing databases, a marked increase in certain clusters of metabolites was observed in the follow-up samples when compared to the case samples and vice versa. These findings suggest the importance of key metabolites in gut health and recovery and enhance understanding of metabolic fluctuations during enteric infections.
Campylobacter commonly causes foodborne infections and antibiotic resistance is an imminent concern. It is not clear, however, if the human gut 'resistome' is affected by Campylobacter during ...infection. Application of shotgun metagenomics on stools from 26 cases with Campylobacter infections and 44 healthy family members (controls) identified 406 unique antibiotic resistance genes (ARGs) representing 153 genes/operons, 40 mechanisms, and 18 classes. Cases had greater ARG richness (p < 0.0001) and Shannon diversity (p < 0.0001) than controls with distinct compositions (p = 0.000999; PERMANOVA). Cases were defined by multidrug resistance genes and were dominated by Proteobacteria (40.8%), specifically those representing Escherichia (20.9%). Tetracycline resistance genes were most abundant in controls, which were dominated by Bacteroidetes (45.3%) and Firmicutes (44.4%). Hierarchical clustering of cases identified three clusters with distinct resistomes. Case clusters 1 and 3 differed from controls containing more urban and hospitalized patients. Relative to family members of the same household, ARG composition among matched cases was mostly distinct, though some familial controls had similar profiles that could be explained by a shorter time since exposure to the case. Together, these data indicate that Campylobacter infection is associated with an altered resistome composition and increased ARG diversity, raising concerns about the role of infection in the spread of resistance determinants.
The gut microbiota in cattle is essential for protein, energy, and vitamin production and hence, microbiota perturbations can affect cattle performance. This study evaluated the effect of ...intramammary (IMM) ceftiofur treatment and lactation stage on the functional gut microbiome and metabolome. Forty dairy cows were enrolled at dry-off. Half received IMM ceftiofur and a non-antibiotic teat sealant containing bismuth subnitrate (cases), while the other half received the teat sealant (controls). Fecal samples were collected before treatment at dry off, during the dry period (weeks 1 and 5) and the first week after calving (week 9). Shotgun metagenomic sequencing was applied to predict microbial metabolic pathways whereas untargeted metabolomics was used identify polar and nonpolar metabolites. Compared to controls, long-term changes were observed in the cows given ceftiofur, including a lower abundance of microbial pathways linked to energy production, amino acid biosynthesis, and other vital molecules. The metabolome of treated cows had elevated levels of stachyose, phosphatidylethanolamine diacylglycerol (PE-DAG), and inosine a week after the IMM ceftiofur application, indicating alterations in microbial fermentation, lipid metabolism, energy, and cellular signaling. Differences were also observed by sampling, with cows in late lactation having more diverse metabolic pathways and a unique metabolome containing higher levels of histamine and histamine-producing bacteria. These data illustrate how IMM ceftiofur treatment can alter the functionality of the hindgut metabolome and microbiome. Understanding how antibiotics and lactation stages, which are each characterized by unique diets and physiology, impact the function of resident microbes is critical to define normal gut function in dairy cattle.
Peer review is central to the scientific process and scientists' career advancement, but bias at various stages of the review process disadvantages some authors. Here we use peer review data from ...312,740 biological sciences manuscripts across 31 studies to (1) examine evidence for differential peer review outcomes based on author demographics, (2) evaluate the efficacy of solutions to reduce bias and (3) describe the current landscape of peer review policies for 541 ecology and evolution journals. We found notably worse review outcomes (for example, lower overall acceptance rates) for authors whose institutional affiliations were in Asia, for authors whose country's primary language is not English and in countries with relatively low Human Development Indices. We found few data evaluating efficacy of interventions outside of reducing gender bias through double-blind review or diversifying reviewer/editorial boards. Despite evidence for review outcome gaps based on author demographics, few journals currently implement policies intended to mitigate bias (for example, 15.9% of journals practised double-blind review and 2.03% had reviewer guidelines that mentioned social justice issues). The lack of demographic equity signals an urgent need to better understand and implement evidence-based bias mitigation strategies.
The human gut environment is replete with host-microbe and microbe-microbe interactions that shape human health. This system is also a known reservoir for antimicrobial resistance (AMR). The ubiquity ...of AMR is alarming, as greater than 2.8 million antibiotic-resistant infections and 35,000 deaths occur annually in the United States. Multiple human pathogens have demonstrated reduced susceptibility to various antibiotics, including enteric pathogens such as Campylobacter, Salmonella, Shigella, and STEC, which cause millions of foodborne infections each year. The increasing incidence of antibiotic resistant enteric infections substantiates a need to further characterize these pathogens’ role in the curation and dissemination of AMR across environments. In this dissertation, a total of 223 human stools were assessed using shotgun metagenomics sequencing to investigate gut microbiome changes associated with enteric infection. Sixty-three stools were collected from patients suffering from enteric infection between 2011-2015 by the Michigan Department of Health and Human Services (MDHHS). Sixty-one of these patients submitted a follow-up sample between 1- and 29-weeks post-infection, and 99 healthy household members also submitted stools to serve as controls. In Chapter 2, a subset of patients infected with Campylobacter spp. and their related controls were investigated to assess the gut resistome, or collection of all antimicrobial resistance genes (ARGs) and their genetic precursors, related to infection. This examination revealed significantly higher ARG diversity in infected patients compared to healthy controls. Specifically, levels of multi-drug resistance (MDR) were greatly increased during infection. Three case clusters with distinct resistomes were identified; two of these clusters had unique ARG profiles that differed from those of healthy family members. In Chapter 3, a larger subset of 120 paired samples (60 infected vs. 60 recovered) were investigated to further characterize resistome and microbiome fluctuations related to infection and recovery. Again, infected patients harbored greater resistome diversity; however, recovered individuals displayed higher diversity in their microbiota composition. Despite their lower overall microbial diversity, patients with acute infections showed an increase in the abundance of members of Enterobacteriaceae, with specific expansion of the genus Escherichia. Host-tracking analysis revealed that many Enterobacteriaceae carried ARGs related to MDR and biocide resistance, a finding with broad implications for the ecology of resistance during infection. The fourth chapter explored metabolic capacity of gut microbial communities. In addition to metabolic pathway prediction, untargeted metabolomics was performed via LC/MS for 122 paired samples. Pathway annotation suggested that infected individuals contain greater microbial functional capacity, but metabolomics indicated greater overall metabolite diversity among recovered patients. Infection was associated with enhanced nitrogen and amino acid metabolism pathways. Although many metabolites remain uncharacterized, their presence or absence among individuals suggest their importance during and after infection. Altogether, the findings of this dissertation further characterize ecological consequences related to enteric infection in the human gut. Specifically, this research illustrates the importance of enteric infection in the dissemination and persistence of resistance determinants. Moreover, the expansion of Enterobacteriaceae and the evident increase in nitrogen- and amino acid-related metabolism during infection represent potential targets for future intervention practices.
Flare frequency distributions represent a key approach to addressing one of the largest problems in solar and stellar physics: determining the mechanism that counter-intuitively heats coronae to ...temperatures that are orders of magnitude hotter than the corresponding photospheres. It is widely accepted that the magnetic field is responsible for the heating, but there are two competing mechanisms that could explain it: nanoflares or Alfvén waves. To date, neither can be directly observed. Nanoflares are, by definition, extremely small, but their aggregate energy release could represent a substantial heating mechanism, presuming they are sufficiently abundant. One way to test this presumption is via the flare frequency distribution, which describes how often flares of various energies occur. If the slope of the power law fitting the flare frequency distribution is above a critical threshold, \(\alpha=2\) as established in prior literature, then there should be a sufficient abundance of nanoflares to explain coronal heating. We performed \(>\)600 case studies of solar flares, made possible by an unprecedented number of data analysts via three semesters of an undergraduate physics laboratory course. This allowed us to include two crucial, but nontrivial, analysis methods: pre-flare baseline subtraction and computation of the flare energy, which requires determining flare start and stop times. We aggregated the results of these analyses into a statistical study to determine that \(\alpha = 1.63 \pm 0.03\). This is below the critical threshold, suggesting that Alfvén waves are an important driver of coronal heating.
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