scholarly journals Investigation of tylosin in feed of feedlot cattle and effects on liver abscess prevalence, and fecal and soil microbiomes and resistomes1

2019 ◽  
Vol 97 (11) ◽  
pp. 4567-4578 ◽  
Author(s):  
Margaret D Weinroth ◽  
Jennifer N Martin ◽  
Enrique Doster ◽  
Ifigenia Geornaras ◽  
Jennifer K Parker ◽  
...  
Keyword(s):  
Liver Abscess ◽  
Soil Microbial Communities ◽  
Amplicon Sequencing ◽  
Feedlot Cattle ◽  
Microbiome Composition ◽  
Soil Microbial ◽  
16S Rrna Amplicon Sequencing ◽  
Liver Abscesses ◽  
Geographical Regions ◽  
Antimicrobial Resistance Genes

Abstract Liver abscesses in feedlot cattle are detrimental to animal performance and economic return. Tylosin, a macrolide antibiotic, is used to reduce prevalence of liver abscesses, though there is variable efficacy among different groups of cattle. There is an increased importance in better understanding the etiology and pathogenesis of this condition because of growing concern over antibiotic resistance and increased scrutiny regarding use of antibiotics in food animal production. The objective of this study was to compare the microbiomes and antimicrobial resistance genes (resistomes) of feces of feedlot cattle administered or not administered tylosin and in their pen soil in 3 geographical regions with differing liver abscess prevalences. Cattle (total of 2,256) from 3 geographical regions were selected for inclusion based on dietary supplementation with tylosin (yes/no). Feces and pen soil samples were collected before harvest, and liver abscesses were identified at harvest. Shotgun and 16S rRNA amplicon sequencing were used to evaluate the soil and feces. Microbiome and resistome composition of feces (as compared by UniFrac distances and Euclidian distances, respectively) did not differ (P > 0.05) among tylosin or no tylosin-administered cattle. However, feedlot location was associated with differences (P ≤ 0.05) of resistomes and microbiomes. Using LASSO, a statistical model identified both fecal and soil microbial communities as predictive of liver abscess prevalence in pens. This model explained 75% of the variation in liver abscess prevalence, though a larger sample size would be needed to increase robustness of the model. These data suggest that tylosin exposure does not have a large impact on cattle resistomes or microbiomes, but instead, location of cattle production may be a stronger driver of both the resistome and microbiome composition of feces.

scholarly journals PSIII-13 Preliminary assessment of the impact of liver abscess presence on stress-related physiological parameters associated with well-being in feedlot cattle

2019 ◽  
Vol 97 (Supplement_3) ◽  
pp. 188-189
Author(s):  
Faith Baier ◽  
Temple Grandin ◽  
Terry Engle ◽  
Lily Edwards-Callaway
Keyword(s):  
Infrared Thermography ◽  
Liver Abscess ◽  
Serum Cortisol ◽  
Well Being ◽  
Feedlot Cattle ◽  
Infrared Analysis ◽  
Hair Cortisol ◽  
Liver Abscesses ◽  
Hair Samples ◽  
The Impact

Abstract Liver abscesses can affect cattle performance, though the impact on well-being is relatively unknown. The purpose of this study was to evaluate the relationship between liver abscess presence and stress-related parameters in feedlot cattle. Three hundred and sixty-three feedlot steers (675 ± 2.3 kg) that were enrolled in a nutrition feeding experiment were allocated to one of three groups based on the liver abscess score assigned after slaughter. The liver abscess scoring groups were: no liver abscess presence (NLA; n = 316); mild liver abscess presence (MLA; n = 21) and severe liver abscess presence (SLA; n = 24). Two animals were unable to be assigned liver abscess scores. Two days prior to slaughter, at the time of weighing, hair samples were collected from the right rump of each animal and analyzed for cortisol concentrations. Additionally, during restraint, infrared thermography was used to quantify eye temperatures and a mobility score was assigned to each animal upon chute exit. During slaughter, exsanguination blood was collected from 115 of the 363 animals and analyzed for serum cortisol concentrations. Cattle were blocked by nutrition feeding treatments and data were analyzed using analyses of variance to determine differences in outcome variables between liver abscess score groups. All animals were included in the infrared analysis and 115 animals were included in the serum and hair cortisol analyses. Infrared thermography (P = 0.55), hair cortisol (P = 0.96), and serum cortisol (P = 0.21) were similar across all liver abscess scores. All animals exhibited normal mobility, thus these values were not included in the analysis. The data indicate that under the conditions of this experiment, liver abscesses did not impact measured stress-related outcomes. Additional research is necessary to understand the impact of liver abscess presence on other stress-related parameters associated with well-being in cattle.

scholarly journals Biological H2 and CO oxidation activities are sensitive to compositional change of soil microbial communities

2020 ◽  
Vol 66 (4) ◽  
pp. 263-273
Author(s):  
Julien Saavedra-Lavoie ◽  
Anne de la Porte ◽  
Sarah Piché-Choquette ◽  
Claude Guertin ◽  
Philippe Constant
Keyword(s):  
Microbial Community ◽  
Microbial Diversity ◽  
Co Oxidation ◽  
Soil Microbial Communities ◽  
Amplicon Sequencing ◽  
Oxidative Capacity ◽  
Rrna Gene ◽  
Soil Microbial Diversity ◽  
Soil Microcosms ◽  
Soil Microbial

Trace gas uptake by microorganisms controls the oxidative capacity of the troposphere, but little is known about how this important function is affected by changes in soil microbial diversity. This article bridges that knowledge gap by examining the response of the microbial community-level physiological profiles (CLPPs), carbon dioxide (CO2) production, and molecular hydrogen (H2) and carbon monoxide (CO) oxidation activities to manipulation of microbial diversity in soil microcosms. Microbial diversity was manipulated by mixing nonsterile and sterile soil with and without the addition of antibiotics. Nonsterile soil without antibiotics was used as a reference. Species composition changed significantly in soil microcosms as a result of dilution and antibiotic treatments, but there was no difference in species richness, according to PCR amplicon sequencing of the bacterial 16S rRNA gene. The CLPP was 15% higher in all dilution and antibiotic treatments than in reference microcosms, but the dilution treatment had no effect on CO2 production. Soil microcosms with dilution treatments had 58%–98% less H2 oxidation and 54%–99% lower CO oxidation, relative to reference microcosms, but did not differ among the antibiotic treatments. These results indicate that H2 and CO oxidation activities respond to compositional changes of microbial community in soil.

scholarly journals Maternal effects on early-life gut microbiome maturation in a wild nonhuman primate

2021 ◽  
Author(s):  
Alice Baniel ◽  
Lauren Petrullo ◽  
Arianne Mercer ◽  
Laurie Reitsema ◽  
Sierra Sams ◽  
...  
Keyword(s):  
Maternal Effects ◽  
Gut Microbiome ◽  
Early Life ◽  
Amplicon Sequencing ◽  
Microbial Colonization ◽  
Fecal Samples ◽  
Microbiome Composition ◽  
16S Rrna Amplicon Sequencing ◽  
Gut Colonization ◽  
First Time

Early-life gut microbial colonization is an important process shaping host physiology, immunity and long-term health outcomes in humans and other animals. However, our understanding of this dynamic process remains poorly investigated in wild animals, where developmental mechanisms can be better understood within ecological and evolutionary relevant contexts. Using 16s rRNA amplicon sequencing on 525 fecal samples from a large cohort of infant and juvenile geladas (Theropithecus gelada), we characterized gut microbiome maturation during the first three years of life and assessed the role of maternal effects in shaping offspring microbiome assembly. Microbial diversity increased rapidly in the first months of life, followed by more gradual changes until weaning. As expected, changes in gut microbiome composition and function with increasing age reflected progressive dietary transitions: in early infancy when infants rely heavily on their mother's milk, microbes that facilitate milk glycans and lactose utilization dominated, while later in development as graminoids are progressively introduced into the diet, microbes that metabolize plant complex polysaccharides became dominant. Furthermore, the microbial community of nursing infants born to first-time (primiparous) mothers was more "milk-oriented" compared to similarly-aged infants born to experienced (multiparous) mothers. Comparisons of matched mother-offspring fecal samples to random dyads did not support vertical transmission as a conduit for these maternal effects, which instead could be explained by slower phenotypic development (and associated slower gut microbiome maturation) in infants born to first-time mothers. Together, our findings highlight the dynamic nature of gut colonization

scholarly journals Coffee Consumption Modulates Amoxicillin-Induced Dysbiosis in the Murine Gut Microbiome

2021 ◽  
Vol 12 ◽  
Author(s):  
Emma Diamond ◽  
Katharine Hewlett ◽  
Swathi Penumutchu ◽  
Alexei Belenky ◽  
Peter Belenky
Keyword(s):  
Gut Microbiome ◽  
Burkholderia Cepacia ◽  
Coffee Consumption ◽  
Amplicon Sequencing ◽  
Antibiotic Use ◽  
Fecal Microbiome ◽  
Microbiome Composition ◽  
16S Rrna Amplicon Sequencing ◽  
Caffeinated Coffee

The microbiome is essential for host health, and perturbations resulting from antibiotic use can lead to dysbiosis and disease. Diet can be a powerful modulator of microbiome composition and function, with the potential to mitigate the negative effects of antibiotic use. Thus, it is necessary to study the impacts of diet and drug interactions on the gut microbiome. Coffee is a commonly consumed beverage containing many compounds that have the potential to affect the microbiome, including caffeine, polyphenols, and fiber. We supplemented mice with caffeinated and decaffeinated coffee in conjunction with amoxicillin, and used 16S rRNA amplicon sequencing of fecal samples to investigate changes in diversity and composition of the murine fecal microbiome. We found that antibiotics, regardless of coffee supplementation, caused significant disruption to the murine fecal microbiome, enriching for Proteobacteria, Verrucomicrobia, and Bacteroidetes, but reducing Firmicutes. While we found that coffee alone did not have a significant impact on the composition of the fecal microbiome, coffee supplementation did significantly affect relative abundance metrics in mice treated with amoxicillin. After caffeinated coffee supplementation, mice treated with amoxicillin showed a smaller increase in Proteobacteria, specifically of the family Burkholderiaceae. Correspondingly we found that in vitro, Burkholderia cepacia was highly resistant to amoxicillin, and that it was inhibited by concentrations of caffeine and caffeinated coffee comparable to levels of caffeine in murine ceca. Overall, this work shows that coffee, and possibly the caffeine component, can impact both the microbiome and microbiome members during antibiotic exposure.

scholarly journals PSIV-19 Relationship between liver abscess microbiome of feedlot cattle and soil organic matter microbiome isolated from feedlot pens

2020 ◽  
Vol 98 (Supplement_4) ◽  
pp. 278-278
Author(s):  
Kathryn E Smith ◽  
Zeno Bester ◽  
Michael E Hubbert ◽  
Clint A Loest
Keyword(s):  
Organic Matter ◽  
Soil Organic Matter ◽  
Liver Abscess ◽  
Variable Region ◽  
The United States ◽  
Feedlot Cattle ◽  
Rrna Gene ◽  
Bacterial Phyla ◽  
Liver Abscesses ◽  
The Impact

Abstract Liver abscess (LA) prevalence has increased 15% for beef cattle and 25% for Holstein cattle. The prevalence of liver abscesses in the Central Plains region (CR) is greater than the Southwest region (SR) of the United States. The objective was to evaluate soil organic matter (SOM) microbiome of feedlot pens, associated LA microbiomes, and the impact of breed, location, and tylosin. Eighty-three commercial feedlot pens were sampled for SOM prior to harvesting and LA samples were collected from two commercial packing plants in Tolleson, AZ (SR) and Greely, CO (CR). Liver abscess samples were linked to SOM samples. Amplification and sequencing of the V4 variable region of the 16S rRNA gene was performed using the Illumina MiSeq. Bacterial phyla, genera, and diversity indices were reported for LA and SOM samples. Reported data is from a subset of five pens. The most prevalent genera identified in liver abscesses were Fusobacterium (64.2%) and Bacteroides (18.6%). Predominant SOM genera were Atopostipes (13%) and Clostridium (10%). Phylum SOM Shannon Weiner Index (SWI) was lower for the CR compared to the SR (0.034 vs. 0.174; P < 0.05), indicating a dominant bacterium in the CR. Atopostipes and Clostridium comprised 48% of the CR SOM, explaining the lower SWI. The SWI of SOM and liver abscesses of Holsteins are lower (P < 0.05) compared to beef counterparts. Additionally, Clostridium, Fusobacterium, and Atopostipes populations were greater (P < 0.05) in SOM of Holstein pens than beef pens. Genus richness was lower (P < 0.05) for both SOM and liver abscesses from pens of cattle fed tylosin vs. no tylosin. There is a negative correlation between SOM SWI and LA% (R2 = -0.49; P = 0.03) and LA severity (A+) (R2 = -0.44; P = 0.05). In conclusion, SOM may serve as a potential vector for liver abscesses.

scholarly journals Microbiome-related aspects of locust density-dependent phase transition

2020 ◽  
Author(s):  
Omer Lavy ◽  
Ohad Lewin-Epstein ◽  
Yonatan Bendett ◽  
Uri Gophna ◽  
Eran Gefen ◽  
...  
Keyword(s):  
Phase Transition ◽  
Old Testament ◽  
Transmission Rate ◽  
Bacterial Species ◽  
Horizontal Transmission ◽  
Amplicon Sequencing ◽  
Bacterial Composition ◽  
Microbiome Composition ◽  
16S Rrna Amplicon Sequencing ◽  
Before And After

AbstractLocust plagues are an ancient phenomenon, with references going back to the Old Testament. These swarming pests are notorious for their tendency to aggregate and perform long migrations, consuming vast amounts of vegetation and decimating the cultivated fields on their path. However, when population density is low, locusts will express a solitary, cryptic, non-aggregating phenotype that is not considered as an agricultural pest. Although transition of locusts from the solitary to the gregarious phase has been well studied, the shifts in the locust microbiome composition associated with this phase-transition have yet to be addressed. Here, using 16S rRNA amplicon sequencing, we compared the bacterial composition of solitary desert locusts before and after a crowding-induced phase-transition. Our findings reveal that the microbiome is altered during the phase transition. We also show that this significant change in bacterial composition includes the acquisition of a specific bacterial species - Weissella cibaria (Firmicutes), which has been previously shown to induce aggregation in cockroaches. Our findings led us to hypothesize that the locust microbiome may play a role in inducing aggregation behavior, contributing to the formation and maintenance of a swarm. Employing a mathematical model, we demonstrate the potential evolutionary advantage of inducing aggregation under various environmental conditions; and specifically, when the aggregation-inducing microbe exhibits a relatively high horizontal transmission rate. This is a first description of a previously unknown and important aspect of locust phase transition, demonstrating that the phase shift includes a shift in the gut and integument bacterial composition.

scholarly journals Anopheles albimanus natural microbiota is altered within one generation of laboratory colonization

2020 ◽  
Author(s):  
Nsa Dada ◽  
Ana Cristina Benedict ◽  
Francisco López ◽  
Juan C. Lol ◽  
Mili Sheth ◽  
...  
Keyword(s):  
First Generation ◽  
Amplicon Sequencing ◽  
Anopheles Albimanus ◽  
Microbiome Composition ◽  
Laboratory Conditions ◽  
16S Rrna Amplicon Sequencing ◽  
Late Instar ◽  
Microbe Interactions ◽  
First Time ◽  
Natural Microbiota

AbstractResearch on mosquito-microbe interactions may lead to new tools for mosquito and mosquito-borne disease control. To date, such research has largely utilized laboratory-reared mosquitoes that typically lack the microbial diversity of wild populations. A logical progression in this area involves working under controlled settings using field-derived mosquitoes or, in most cases, their progeny. Thus, an understanding of how laboratory colonization affects the assemblage of mosquito microbiota would aid in advancing mosquito microbiome studies and their applications beyond laboratory settings. Using high throughput 16S rRNA amplicon sequencing, we characterized the internal and cuticle surface microbiota of F1 progeny of wild-caught adult Anopheles albimanus from four locations in Guatemala. A total of 132 late instar larvae and 135 2-5day old, non-blood-fed virgin adult females that were reared under identical laboratory conditions, were pooled (3 individuals/pool) and analyzed. F1 larvae from different maternal sites showed different microbial compositions (p=0.001; F = 9.5), but these differences were absent at the adult stage (p=0.12; F =1.6). These results suggest that field-acquired mosquito microbiota may be lost in as early as the first generation of colonization under normal laboratory conditions, thus, requiring adjustments to maintain field-derived microbiota. This is the first time that the microbiota of F1 progeny of wild-caught mosquitoes has been characterized in relation to maternal collection site. Our findings provide a comprehensive background for studying how parentage and environmental conditions differentially or concomitantly affect mosquito microbiome composition, and how this can be exploited in advancing mosquito microbiome studies and their applications beyond laboratory settings.

scholarly journals Analysis of soil microbial communities based on amplicon sequencing of marker genes

2017 ◽  
Vol 53 (5) ◽  
pp. 485-489 ◽  
Author(s):  
Anne Schöler ◽  
Samuel Jacquiod ◽  
Gisle Vestergaard ◽  
Stefanie Schulz ◽  
Michael Schloter
Keyword(s):  
Microbial Communities ◽  
Soil Microbial Communities ◽  
Amplicon Sequencing ◽  
Marker Genes ◽  
Soil Microbial

scholarly journals Soil microbial communities of three grassland ecosystems in the Bayinbuluke, China

2018 ◽  
Vol 64 (3) ◽  
pp. 209-213 ◽  
Author(s):  
Keqiang Shao ◽  
Guang Gao
Keyword(s):  
Microbial Community ◽  
Soil Microbial Community ◽  
Soil Microbial Communities ◽  
Soil Nutrient ◽  
Amplicon Sequencing ◽  
Shannon Index ◽  
Alpine Grassland ◽  
Cold Desert ◽  
Soil Microbial Community Structure ◽  
Soil Microbial

The microbial community plays an important role in soil nutrient cycles and energy transformations in alpine grassland. In this study, we investigated the composition of the soil microbial community collected from alpine cold swamp meadow (ASM), alpine cold meadow (AM), and alpine cold desert steppe (ADS) within the Bayinbuluke alpine grassland, China, using Illumina amplicon sequencing. Of the 147 271 sequences obtained, 36 microbial phyla or groups were detected. The results showed that the ADS had lower microbial diversity than the ASM and AM, as estimated by the Shannon index. The Verrucomicrobia, Chloroflexi, Planctomycetes, Proteobacteria, and Actinobacteria were the predominant phyla in all 3 ecosystems. Particularly, Thaumarchaeota was only abundant in ASM, Bacteroidetes in AM, and Acidobacteria in ADS. Additionally, the predominant genus also differed with each ecosystem. Candidatus Nitrososphaera was predominant in ADS, the Pir4 lineage in ASM, and Sphingomonas in AM. Our results indicated that the soil microbial community structure was different for each grassland ecosystem in the Bayinbuluke.

scholarly journals Changes in soil microbial communities at Jinsha earthen site are associated with earthen site degradation

2019 ◽  
Author(s):  
Jing Li ◽  
Xiaoyue Zhang ◽  
Lin Xiao ◽  
Ke Liu ◽  
Yue Li ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Soil Microbial Communities ◽  
Amplicon Sequencing ◽  
Biological Factor ◽  
Rrna Gene ◽  
Biological Factors ◽  
Soil Microbial ◽  
Relative Abundances ◽  
Bacteria And Fungi ◽  
Degree Of Degradation

Abstract Background: Jinsha earthen site in Chengdu, China, plays an important role in understanding the ancient culture and history of Shu civilization. The site is undergoing soil degradation due to physical, chemical and biological factors, while very little is known about the influence of biological factors on earthen sites. To investigate the biological factor, we analyzed microbial communities and physicochemical properties from samples with no obvious, mild, moderate and severe degradation, referred to as S1, S2, S3 and S4 sample groups, respectively.Results: Amplicon sequencing targeting the 16S rRNA gene and ITS for bacteria and fungi, respectively, revealed high bacterial and relatively low fungal diversity; the bacterial OTUs were assigned into 36 phyla and 617 genera and the fungal OTUs into 5 phyla and 205 genera. The relative abundances of Bacteroidetes, Proteobacteria and Firmicutes were higher and that of Actinobacteria lower with higher degree of degradation. In the genus level, the relative abundances of Bacteroides and Ralstonia were higher and that of Rubrobacter lower with higher degree of degradation. The distribution of the fungal genera in the four sample groups seemed more random than that of bacteria; however, the relative abundance of the yeast genus Candida was highest in the severely degraded sample group. For both bacteria and fungi, the differences in community composition were associated with differences in EC, moisture, pH, and the concentrations of NH 4 + , K + , Mg 2+ , Ca 2+ and SO 4 2- .Conclusion: Taken together, the microbial communities in soil with different degree of degradation were distinctly different at Jinsha earthen site, and degradation was accompanied with bigger changes in the bacterial than in the fungal community.

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