Biology subjects

Suen, G.

Publications and source records attributed to Suen, G..

14 recordsLinked to original sources

bioRxiv2026

Antimicrobial use contributes to resistance gene enrichment across cattle groups on commercial dairy farms

Antimicrobial use (AMU) in agricultural systems is frequently linked to antimicrobial resistance (AMR). Yet, the scale at which AMU reshapes host-associated resistomes remains unclear. This gap arises, in part, from the scarcity of farm-level AMU data from commercial production systems. Here, we combine detailed AMU records from commercial dairy farms with metagenomic analyses of bovine fecal resistomes from calves, lactating cows, sick cows, and cull cows. At a broad level, resistome profiles were similar regardless of farm AMU. Resistance associated with historically common antibiotics, such as tetracyclines, was frequent on low- and high-AMU farms, indicating that some resistance classes are ubiquitous in dairy systems regardless of current AMU. In contrast, resistance to other drug classes varied systematically with AMU. Higher AMU was associated with increased resistance to aminoglycosides, {beta}-lactams, and macrolides, drug classes that are critical for treating mastitis and bovine respiratory disease. Resistance gene richness and diversity were highest in calves, underscoring the importance of accounting for host traits alongside AMU when evaluating resistance patterns. Together, these findings underscore the need for detailed, farm-level AMU data to understand how management practices shape AMR and to inform strategies for sustaining the effectiveness of existing antimicrobials in agricultural and public-health contexts.

genomics↗

bioRxiv2025

Patterns of Microbial Succession and Niche Differentiation Across Depth and Age in a Landfill Have Implications for Management Strategies

Despite microorganisms being primarily responsible for landfill material decomposition, limited characterization has been performed across both landfill depth and age. Here, we investigated the microbial communities and physicochemical parameters in two active and two closed landfill wells from surface to bottom, as well as fill dirt and leachate at a sanitary landfill near Madison, Wisconsin, USA. Amplicon community sequencing fungi, bacteria and archaea revealed distinct microbial community structures across landfill sites. The observed patterns of microbial community succession by depth and age mirror the known phases of the landfill life cycle. Younger surface samples were dominated by aerobic fungi, which transitioned to fermentative bacteria and methanogenic archaea in older, deeper, layers. Simultaneously, high species richness was preserved across landfill ages, while reduced evenness at specific depths support spatial niche differentiation. In conjunction with the lack of trends found for physicochemical parameters by depth, this supports niche differentiation driven by the highly heterogenous waste inputs. This study provides the first comprehensive vertical profile of bacterial, fungal, and archaeal communities across landfill depths and ages, highlighting the influence of these parameters on physicochemical factors and microbial distribution within landfills. These results have implications for improving landfill management, including renewable gas energy production, minimizing emissions, and increasing degradation rates.

microbiology↗

bioRxiv2025

Host-microbe mutualism drives urea carbon salvage and acetogenesis during hibernation

2.Hibernation is a seasonal survival strategy employed by certain mammals that, through torpor use, reduces overall energy expenditure and permits long-term fasting. Although fasting solves the challenge of winter food scarcity, it also removes dietary carbon, a critical biomolecular building block. Here, we demonstrate a process of urea carbon salvage (UCS) in hibernating 13-lined ground squirrels, whereby urea carbon is reclaimed through gut microbial ureolysis and used in reductive acetogenesis to produce acetate, a short-chain fatty acid (SCFA) of major value to the host and its gut microbiota. We find that urea carbon incorporation into acetate is more efficient during hibernation than the summer active season, and that while both host and gut microbes oxidize acetate for energy supply throughout the year, the hosts ability to absorb and oxidize acetate is highest during hibernation. Metagenomic analysis of the gut microbiome indicates that genes involved in the degradation of gut mucins, an abundant endogenous nutrient, are retained during hibernation. The hydrogen disposal associated with reductive acetogenesis from urea carbon helps facilitate this mucin degradation by providing a luminal environment that sustains fermentation, thereby generating SCFAs and other metabolites usable by both the host and its gut microbes. Our findings introduce UCS as a mechanism that enables hibernating squirrels and their gut microbes to exploit two key endogenous nutrient sources - urea and mucins - in the resource-limited hibernation season. 3. SIGNIFICANCE STATEMENTWhen food becomes scarce during winter, hibernating mammals induce torpor to minimize energy demands and enable monthslong fasting. However, fasting eliminates the intake of essential nutrients such as carbon. We identified a two-step microbial-host interaction in ground squirrels - urea carbon salvage (UCS) - which counters carbon limitation by salvaging carbon from waste urea. Through activities of ureolytic and acetogenic bacteria, urea-derived CO2 is reduced by free hydrogen to form acetate, whose oxidation provides energy for gut microbes and the host. This process also helps maintain a permissive environment for fermentation of other host-derived, energy-dense compounds such as mucins. UCS broadens our understanding of host-microbe mutualism under extreme nutritional constraints and may represent a widespread adaptation among fasting mammals.

physiology↗

bioRxiv2024

The microbiota of wooden cheese ripening boards is a rich source of antimicrobial-producing bacteria against Listeria monocytogenes

Wooden boards are essential tools in cheese ripening and there are accumulating observations suggesting their antimicrobial effect against foodborne bacterial pathogens, such as Listeria monocytogenes. However, poor bacterial recovery of bacteria from wood can confound quantification of pathogen burdens. To assess L. monocytogenes survival on wooden cheese boards, we applied a disruptive grinding method and tracked native board-associated bacterial counts as controls. Our data revealed that L. monocytogenes declines on clean zones of wooden boards, but can replicate on areas where there is suitable cheese. Our microbiota analysis revealed diverse bacterial communities on wooden board surfaces, with a prominent presence of Brevibacterium, Brachybacterium, and Staphylococcus genera. We further identified seven bacterial species that inhibit L. monocytogenes, belonging to Bacillus, Staphylococcus, and Serratia phyla, as well as Lactococcus lactis. We focused on a Bacillus safensis isolate as a novel biocontrol agent candidate, and found it to potently inhibit L. monocytogenes via secreted antimicrobial factors. Our genomic, bioinformatic, and biochemical analyses indicate that those factors are likely antimicrobial peptides encoded by multiple biosynthetic gene clusters, several of which are unique to B. safensis and have not been characterized. A sub-inhibitory concentration of B. safensis supernatant induces a significant down-regulation of prophage elements and up-regulation antimicrobial stress response in L. monocytogenes. Taken together, our findings indicate that the wooden board microbiota is a rich source of antimicrobial-producing bacteria with potential applications in foodborne pathogen control strategies. IMPORTANCEDespite stringent food safety measures, L. monocytogenes foodborne outbreaks remain frequent with high hospitalization and mortality rates. Removal of L. monocytogenes from food processing environments is extremely challenging, because this pathogen is ubiquitous and encodes a wide array of stress response mechanisms that enable it to thrive under harsh conditions. Our study found that clean wooden boards used in cheese ripening inhibit L. monocytogenes, causing a noticeable decline in pathogen population following surface inoculation. Bacterial communities on wooden cheese boards are rich and diverse, and harbor many species that produce antimicrobial compounds against L. monocytogenes, with the example of a new B. safensis isolate. Therefore, wooden board microbiota is a promising source for future antimicrobial discovery efforts.

microbiology↗

bioRxiv2024

Opportunistic pathogens are prevalent across the culturable exogenous and endogenous microbiota of stable flies captured at a dairy facility

Stable flies in the genus Stomoxys are highly abundant, blood-feeding pests on dairy farms; however, their role in the carriage and potential transmission of pathogens is largely understudied. Here, we report on the frequency and distribution of culturable bacteria collected from Stomoxys flies captured in free stall barns and nearby calf hutches over a three-month period on a focal research farm in Wisconsin, USA. Mastitis-associated bacterial taxa, including Staphylococcus, Escherichia, Enterobacter, and Klebsiella spp., were frequently isolated from pooled samples of the internal or external portions of the flies. Conversely, selective enrichment protocols from these samples yielded only a single isolate of Salmonella and no enterohemorrhagic Escherichia coli O157. Neither trap location nor time of capture had a significant impact on the observed frequency of most bacterial genera isolated from the flies. Our results confirm that Stomoxys flies harbor both mastitis-associated bacterial taxa and bacterial taxa associated with opportunistic infections in humans. Further research into the transmission of fly-associated microbes could be important in the control of mastitis or other bacterial diseases on dairy farms.

microbiology↗

bioRxiv2024

Sensitivity of dairy calf Salmonella enterica serotype Cerro isolates to infection-relevant stressors

Salmonella enterica serotype Cerro (S. Cerro) is an emerging Salmonella serotype isolated from cattle, but the association of S. Cerro with disease is not well understood. While comparative genomic analyses of bovine S. Cerro isolates have indicated mutations in elements associated with virulence, the correlation of S. Cerro fecal shedding with clinical disease in cattle varies between epidemiologic studies. The primary objective of this study was to characterize the infection-relevant phenotypes of S. Cerro fecal isolates obtained from neonatal calves born on a dairy farm in Wisconsin, USA. The S. Cerro isolates varied in biofilm production and sensitivity to the bile salt deoxycholate. All S. Cerro isolates were sensitive to sodium hypochlorite, hydrogen peroxide, and acidic shock. However, S. Cerro isolates were resistant to nitric oxide stress. Two S. Cerro isolates were unable to compete with S. Typhimurium during infection of calf ligated intestinal loops, indicating decreased fitness in vivo. Together, our data suggest that S. Cerro is sensitive to some innate antimicrobial defenses present in the gut, many of which are also used to control Salmonella in the environment. The observed phenotypic variation in S. Cerro isolates from a single farm suggest phenotypic plasticity that could impact infectious potential, transmission, and persistence on a farm. ImportanceSalmonella enterica is a zoonotic pathogen that threatens both human and animal health. Salmonella enterica serotype Cerro is being isolated from cattle at increasing frequency over the past two decades, however its association with clinical disease is unclear. The goal of this study was to characterize infection-relevant phenotypes of S. Cerro isolates obtained from dairy calves from a single farm. Our work shows that there can be variation among temporally-related S. Cerro isolates and that these isolates are sensitive to killing by toxic compounds of the innate immune system and those used for environmental control of Salmonella. This work contributes to our understanding of the pathogenic potential of the emerging pathogen S. Cerro.

microbiology↗

bioRxiv2023

Disturbance-Diversity Relationships of Microbial Communities Change Based on Growth Substrate

Disturbance events can impact ecological community dynamics. Understanding how communities respond to disturbances, and how those responses can vary, is a challenge in microbial ecology. In this study, we grew a previously enriched specialized microbial community on either cellulose or glucose as a sole carbon source, and subjected them to one of five different disturbance regimes of varying frequencies ranging from low to high. Using 16S rRNA gene amplicon sequencing, we show that community structure is largely driven by substrate, but disturbance frequency affects community composition and successional dynamics. When grown on cellulose, bacteria in the genera Cellvibrio, Lacunisphaera, and Asticaccacaulis are the most abundant microbes. However, Lacunisphaera is only abundant in the lower disturbance frequency treatments, while Asticaccaulis is more abundant in the highest disturbance frequency treatment. When grown on glucose, the most abundant microbes are two Pseudomonas sequence variants, and a Cohnella sequence variant that is only abundant in the highest disturbance frequency treatment. Communities grown on cellulose exhibited a greater range of diversity (0.67-1.99 Shannon diversity and 1.38-5.25 Inverse Simpson diversity) that peak at the intermediate disturbance frequency treatment, or 1 disturbance every 3 days. Communities grown on glucose, however, ranged from 0.49-1.43 Shannon diversity and 1.37-3.52 Inverse Simpson with peak diversity at the greatest disturbance frequency treatment. These results demonstrate that the dynamics of a microbial community can vary depending on substrate and the disturbance frequency, and may potentially explain the variety of diversity-disturbance relationships observed in microbial ecosystems. Abstract ImportanceA generalizable diversity-disturbance relationship (DDR) of microbial communities remains a contentious topic. Various microbial systems have different DDRs. Rather than finding support or refuting specific DDRs, we investigated the underlying factors that lead to different DDRs. In this study, we measured a cellulose-enriched microbial communitys response to a range of disturbance frequencies from high to low, across two different substrates: cellulose and glucose. We demonstrate that the community displays a unimodal DDR when grown on cellulose, and a monotonically increasing DDR when grown on glucose. Our findings suggest that the same community can display different DDRs. These results suggest that the range of DDRs we observe across different microbial systems may be due to the nutritional resources microbial communities can access and the interactions between bacteria and their environment.

microbiology↗

bioRxiv2023

Determinants of Gastrointestinal Group B Streptococcus Carriage in Adults

BackgroundStreptococcus agalactiae (Group B Streptococcus, GBS) is a commensal Gram-positive bacterium found in the human gastrointestinal and urogenital tracts. Much of what is known about GBS relates to the diseases it causes in pregnant people and neonates. However, GBS is a common cause of disease in the general population with 90% of GBS mortality occurring in non-pregnant people. There are limited data about the predisposing factors for GBS and the reservoirs in the body. To gain an understanding of the determinants of gastrointestinal GBS carriage, we used stool samples and associated metadata to determine the prevalence and abundance of GBS in the gut microbiome of adults and find risk factors for GBS status. MethodsWe used 754 stool samples collected from adults in Wisconsin from 2016-2017 to test for the prevalence and abundance of GBS using a Taqman probe-based qPCR assay targeting two GBS-specific genes: cfp and sip. We compared the microbiome compositions of the stool samples by GBS status using 16S rRNA analysis. We compared associations with GBS status and 557 survey variables collected during sample acquisition (demographics, diet, overall health, and reproductive health) using univariate and multivariate analyses. ResultsWe found 137/754 (18%) of participants had detectable GBS in their stool samples with a median abundance of 104 copies per nanogram of starting DNA. There was no difference in GBS status or abundance based on gender. Beta-diversity, Bray-Curtis and Unweighted UniFrac, was significantly different based on carrier status of the participant. Prior to p-value correction, 59/557 (10.6%) survey variables were significantly associated with GBS carrier status and 11/547 (2.0%) variables were significantly associated with abundance (p-value<0.05). After p-value correction, 2/547 (0.4%) variables were associated with GBS abundance: an increased abundance of GBS was associated with a decreased frequency since last dental checkup (p<0.001) and last dental cleaning (p<0.001). Increased GBS abundance was significantly associated with increased frequency of iron consumption (p=0.007) after p-value correction in multivariate models. ConclusionsGBS is found in stool samples from adults in Wisconsin at similar frequencies as pregnant individuals screened with rectovaginal swabs. We did not find associations between risk factors historically associated with GBS in pregnant people, suggesting that risk factors for GBS carriage in pregnancy may differ from those in the general population. We found that frequency of iron consumption and dental hygiene are risk factors for GBS carriage in Wisconsin adults. Given that these variables were not assayed in previous GBS surveys, it is possible they also influence carriage in pregnant people. Taken together, this work serves as a foundation for future work in developing approaches to decrease GBS abundance in carriers.

microbiology↗

bioRxiv2021

Urea nitrogen recycling via gut symbionts increases in hibernators over the winter fast

Hibernation is a mammalian strategy that uses metabolic plasticity to reduce energy demands and enable long-term fasting. Fasting mitigates winter food scarcity but eliminates dietary nitrogen, jeopardizing body protein balance. Here, we reveal gut microbiome-mediated urea nitrogen recycling in hibernating 13-lined ground squirrels (TLGS). Ureolytic gut microbes incorporate urea nitrogen into organic compounds that are absorbed by the host, with the nitrogen reincorporated into the TLGS protein pool. Urea nitrogen recycling is greatest after prolonged fasting in late winter, when urea transporter abundance in gut tissue and urease gene abundance in the microbiome are highest. These results reveal a functional role for the gut microbiome in hibernation and suggest mechanisms by which urea nitrogen recycling contributes to protein balance in other monogastric animals, including humans. One Sentence SummaryGround squirrels and their gut symbionts benefit from urea nitrogen recycling throughout hibernation.

physiology↗

bioRxiv2020

Multiplexed competition in a synthetic squid light organ microbiome using barcode-tagged gene deletions

Beneficial symbioses between microbes and their eukaryotic hosts are ubiquitous and have widespread impacts on host health and development. The binary symbiosis between the bioluminescent bacterium Vibrio fischeri and its squid host Euprymna scolopes serves as a model system to study molecular mechanisms at the microbe-animal interface. To identify colonization factors in this system, our lab previously conducted a global transposon insertion sequencing (INSeq) screen and identified over 300 putative novel squid colonization factors in V. fischeri. To pursue mechanistic studies on these candidate genes, we present an approach to quickly generate barcode-tagged gene deletions and perform high-throughput squid competition experiments with detection of the proportion of each strain in the mixture by barcode sequencing (BarSeq). Our deletion approach improves on previous techniques based on splicing-by-overlap extension PCR (SOE-PCR) and tfoX-based natural transformation by incorporating a randomized barcode that results in unique DNA sequences within each deletion scar. Amplicon sequencing of the pool of barcoded strains before and after colonization faithfully reports on known colonization factors and provides increased sensitivity over colony counting methods. BarSeq enables rapid and sensitive characterization of the molecular factors involved in establishing the Vibrio-squid symbiosis and provides a valuable tool to interrogate the molecular dialogue at microbe-animal host interfaces. ImportanceBeneficial microbes play essential roles in the health and development of their hosts. However, the complexity of animal microbiomes and general genetic intractability of their symbionts have made it difficult to study the coevolved mechanisms for establishing and maintaining specificity at the microbe-animal host interface. Model symbioses are therefore invaluable for studying the mechanisms of beneficial microbe-host interactions. Here we present a combined barcode-tagged deletion and BarSeq approach to interrogate the molecular dialogue that ensures specific and reproducible colonization of the Hawaiian bobtail squid by Vibrio fischeri. The ability to precisely manipulate the bacterial genome, combined with multiplex colonization assays, will accelerate the use of this valuable model system for mechanistic studies of how environmental microbes--both beneficial and pathogenic--colonize specific animal hosts.

microbiology↗

bioRxiv2020

Validating the use of bovine buccal sampling as a proxy for the rumen microbiota using a time course and random forest classification approach

Analysis of the cow microbiome, as well as host genetic influences on the establishment and colonization of the rumen microbiota, is critical for development of strategies to manipulate ruminal function toward more efficient and environmentally friendly milk production. To this end, the development and validation of noninvasive methods to sample the rumen microbiota at a large-scale is required. Here, we further optimized the analysis of buccal swab samples as a proxy for direct microbial samples of the rumen of dairy cows. To identify an optimal time for sampling, we collected buccal swab and rumen samples at six different time points relative to animal feeding. We then evaluated several biases in these samples using a machine learning classifier (random forest) to select taxa that discriminate between buccal swab and rumen samples. Differences in the Simpsons diversity, Shannons evenness and Bray-Curtis dissimilarities between methods were significantly less apparent when sampling was performed prior to morning feeding (P<0.05), suggesting that this time point was optimal for representative sampling. In addition, the random forest classifier was able to accurately identify non-rumen taxa, including 10 oral and feed-associated taxa. Two highly prevalent (> 60%) taxa in buccal and rumen samples had significant variance in absolute abundance between sampling methods, but could be qualitatively assessed via regular buccal swab sampling. This work not only provides new insights into the oral community of ruminants, but further validates and refines buccal swabbing as a method to assess the rumen microbiota in large herds. IMPORTANCEThe gastrointestinal tract of ruminants harbors a diverse microbial community that coevolved symbiotically with the host, influencing its nutrition, health and performance. While the influence of environmental factors on rumen microbes is well-documented, the process by which host genetics influences the establishment and colonization of the rumen microbiota still needs to be elucidated. This knowledge gap is due largely to our inability to easily sample the rumen microbiota. There are three common methods for rumen sampling but all of them present at least one disadvantage, including animal welfare, sample quality, labor, and scalability. The development and validation of non-invasive methods, such as buccal swabbing, for large-scale rumen sampling is needed to support studies that require large sample sizes to generate reliable results. The validation of buccal swabbing will also support the development of molecular tools for the early diagnosis of metabolic disorders associated with microbial changes in large herds.

microbiology↗

bioRxiv2019

Biogeography and Microscale Diversity Shape the Biosynthetic Potential of Fungus-growing Ant-associated Pseudonocardia

The geographic and phylogenetic scale of ecologically relevant microbial diversity is still poorly understood. Using a model mutualism, fungus-growing ants and their defensive bacterial associate Pseudonocardia, we analyzed genetic diversity and biosynthetic potential in 46 strains isolated from ant colonies in a 20km transect near Barro Colorado Island in Panama. Despite an average pairwise core genome similarity of greater than 99%, population genomic analysis revealed several distinct bacterial populations matching ant host geographic distribution. We identified both genetic diversity signatures and divergent genes distinct to each lineage. We also identify natural product biosynthesis clusters specific to isolation locations. These geographic patterns were observable despite the populations living in close proximity to each other and provides evidence of ongoing genetic exchange. Our results add to the growing body of literature suggesting that variation in traits of interest can be found at extremely fine phylogenetic scales.

microbiology↗

bioRxiv2018

Assignment of virus and antimicrobial resistance genes to microbial hosts in a complex microbial community by combined long-read assembly and proximity ligation

The characterization of microbial communities by metagenomic approaches has been enhanced by recent improvements in short-read sequencing efficiency and assembly algorithms. We describe the results of adding long-read sequencing to the mix of technologies used to assemble a highly complex cattle rumen microbial community, and compare the assembly to current short read-based methods applied to the same sample. Contigs in the long-read assembly were 7-fold longer on average, and contained 7-fold more complete open reading frames (ORF), than the short read assembly, despite having three-fold lower sequence depth. The linkages between long-read contigs, provided by proximity ligation data, supported identification of 188 novel viral-host associations in the rumen microbial community that suggest cross-species infectivity of specific viral strains. The improved contiguity of the long-read assembly also identified 94 antimicrobial resistance genes, compared to only seven alleles identified in the short-read assembly. Overall, we demonstrate a combination of experimental and computational methods that work synergistically to improve characterization of biological features in a highly complex rumen microbial community.

microbiology↗

bioRxiv2018

Diet influences early microbiota development in dairy calves without long-term impacts on milk production

Gastrointestinal tract (GIT) microorganisms play important roles in the health of ruminant livestock and impact production of agriculturally relevant products, including milk and meat. Despite this link, interventions to alter the adult microbiota to improve production have proven ineffective as established microbial communities are resilient to change. In contrast, developing communities in young animals may be more easily altered but are less well-studied. Here, we measured the GIT-associated microbiota of 45 Holstein dairy cows from 2 weeks to first lactation using Illumina amplicon sequencing of bacterial (V4 16S), archaeal (V6-8 16S), and fungal (ITS1) communities. Fecal and rumen microbiota were correlated to growth and milk production of animals raised on calf starter grains and/or corn silage to determine if early-life diet has long-term impacts. Significant diet-associated differences in total microbial communities and specific taxa were observed by weaning (8 weeks), but all animals reached an adult-like composition between weaning and 1-year. While some calf diet-driven differences were apparent in the microbiota of adult cows, these dissimilarities did not correlate with animal growth or milk production. This suggests that initial microbial community establishment is impacted by early-life diet, but post-weaning factors have a greater influence on adult communities and production outcomes.\n\nSIGNIFICANCEThe gut microbiota is essential to the survival of many organisms, including ruminants that rely on microorganisms for nutrient acquisition from dietary inputs toward the production of products like milk and meat. While alteration of the adult ruminant microbiota to improve production is possible, changes are often unstable and fail to persist. In contrast, the early-life microbiota may be more amenable to sustained modification; however, few studies have determined the impacts of early-life interventions on downstream production. Here, we investigated the impacts of agriculturally relevant calf diets, including calf starter and corn silage, on gut microbial communities, animal growth, and production through the first lactation cycle. Thus, this work serves to further our understanding of early-life microbiota acquisition as well as informs future practices in livestock management.

microbiology↗