Effects of treatment with enrofloxacin or tulathromycin on fecal microbiota composition and function of dairy calves

AbstractThe increasing concerns with antimicrobial resistance highlights the need for studies evaluating the impacts of antimicrobial use in livestock on antimicrobial resistance using new sequencing technologies. Through shotgun sequencing, we investigated the changes in the fecal microbiome composition and function, with a focus on functions related to antimicrobial resistance, of dairy calves. Heifers 2 to 3 weeks old, which were not treated with antibiotics by the farm before enrollment, were randomly allocated to one of three study groups: control (no treatment), enrofloxacin, or tulathromycin. Fecal samples were collected at days 4, 14, 56 and 112 days after enrollment, and DNA extraction and sample preparation and sequencing was conducted. The effect of antibiotic treatment on each taxon and functional level by time (including Day 0 as a covariate) revealed few changes in the microbiota. At the genus level, enrofloxacin group had higher abundance of Blautia, Coprococcus and Desulfovibrio and lower abundance of Bacteroides when compared to other treatment groups. The SEED database was used for functional analyses, which showed that calves in the enrofloxacin group started with a higher abundance of “Resistance to antibiotics and toxic compounds” function on Day 0, however an increase in antibiotic resistance genes after treatment with enrofloxacin was not observed. “Resistance to Fluoroquinolones” and “Erythromycin resistance”, of relevance given the study groups, were not statistically different in abundance between treatment groups. “Resistance to fluoroquinolones” increased during the study period regardless of treatment group. Despite small differences over the first weeks between treatment groups, at Day 112 the microbiota composition and functional profile was similar among all study groups. These findings show that metaphylaxis treatment of dairy calves with either enrofloxacin or tulathromycin have minimal impacts on the microbial composition and functional microbiota of dairy calves over time.

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Differences in Fecal Microbiome and Antimicrobial Resistance between Captive and Free-Range Sika Deer under the Same Exposure of Antibiotic Anthelmintics

Microbiology Spectrum ◽

10.1128/spectrum.01918-21 ◽

2021 ◽

Author(s):

Kangqi Wu ◽

Yongtao Xu ◽

Weiwei Zhang ◽

Huirong Mao ◽

Biao Chen ◽

...

Keyword(s):

Antimicrobial Resistance ◽

Microbial Communities ◽

Sika Deer ◽

Microbial Composition ◽

Fecal Microbiome ◽

Free Range ◽

And Function ◽

Metagenomic Approach

We used a metagenomic approach to investigate whether and how captive and free-range impact the microbial communities and antimicrobial resistance in sika deer. The results provide solid evidence of the significant impacts on the microbial composition and function in captive and free-range sika deer. Interestingly, although the sika deer had the same exposure to antibiotic anthelmintics, the antimicrobial resistances were affected by the breeding environment.

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The impacts of feeding milk with antibiotics on the fecal microbiome and antibiotic resistance genes in dairy calves

Canadian Journal of Animal Science ◽

10.1139/cjas-2018-0202 ◽

2020 ◽

Vol 100 (1) ◽

pp. 69-76

Author(s):

Xin Feng ◽

Heather M. Littier ◽

Katharine F. Knowlton ◽

Emily Garner ◽

Amy Pruden

Keyword(s):

Antibiotic Resistance ◽

Resistance Genes ◽

Antibiotic Resistance Genes ◽

Dairy Calves ◽

Future Research ◽

Fecal Microbiome ◽

Cell Functions ◽

Whole Milk ◽

Waste Milk ◽

Negative Impacts

The effects of ingestion of antibiotics on the microbiome of the young calf are not well understood. The objective of this study was to evaluate the effect of feeding milk containing pirlimycin on the prevalence of antibiotic resistance genes in the fecal microbiome of dairy calves using a metagenomic approach. In this study calves were assigned to either pasteurized whole milk (control; n = 5) or pasteurized whole milk containing 0.2 mg L−1 of pirlimycin (treatment; n = 5). Fecal samples were collected on days 1, 42, and 84. Functional analysis of DNA via metagenomic rapid annotations using subsystems technology revealed that pirlimycin had no effects on abundance of sequences coding for different cell functions except in the “phage, prophage, and transposable elements” category. Evaluation of the major antibiotic resistance types in samples via annotation against the Comprehensive Antibiotic Resistance Database analysis showed no difference between the two groups. The results of this study will help assess the risk of use of antibiotics in animal agriculture and increase our understanding of how antibiotics present in waste milk affects both calves and their manure, and will lay the groundwork for future research on manure treatment or other strategies to minimize any negative impacts.

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The gut microbiota composition of Trichoplusia ni is altered by diet and may influence its polyphagous behavior

Scientific Reports ◽

10.1038/s41598-021-85057-0 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

M. Leite-Mondin ◽

M. J. DiLegge ◽

D. K. Manter ◽

T. L. Weir ◽

M. C. Silva-Filho ◽

...

Keyword(s):

Trichoplusia Ni ◽

Artificial Diet ◽

Structure And Function ◽

Microbiota Composition ◽

Potential Mechanism ◽

Microbial Composition ◽

Plant Pests ◽

Insect Gut ◽

And Function ◽

Gut Microbiota Composition

AbstractInsects are known plant pests, and some of them such as Trichoplusia ni feed on a variety of crops. In this study, Trichoplusia ni was fed distinct diets of leaves of Arabidopsis thaliana or Solanum lycopersicum as well as an artificial diet. After four generations, the microbial composition of the insect gut was evaluated to determine if the diet influenced the structure and function of the microbial communities. The population fed with A. thaliana had higher proportions of Shinella, Terribacillus and Propionibacterium, and these genera are known to have tolerance to glucosinolate activity, which is produced by A. thaliana to deter insects. The population fed with S. lycopersicum expressed increased relative abundances of the Agrobacterium and Rhizobium genera. These microbial members can degrade alkaloids, which are produced by S. lycopersicum. All five of these genera were also present in the respective leaves of either A. thaliana or S. lycopersicum, suggesting that these microbes are acquired by the insects from the diet itself. This study describes a potential mechanism used by generalist insects to become habituated to their available diet based on acquisition of phytochemical degrading gut bacteria.

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Gut metagenomics discriminates unique microbial signatures in diverse symptomatic profiles with attention-deficit/hyperactivity disorder

10.21203/rs.3.rs-28862/v1 ◽

2020 ◽

Author(s):

Yan Li ◽

Haiting Sun ◽

Yufen Huang ◽

Anqi Yin ◽

Ping Wang ◽

...

Keyword(s):

Antibiotic Resistance ◽

Gut Microbiota ◽

Vitamin B6 ◽

Serum Vitamin ◽

Microbiota Composition ◽

Microbial Composition ◽

Hyperactivity Disorder ◽

Metabolic Functions ◽

And Function ◽

Early Life Events

Abstract BackgroundAttention-deficit/hyperactivity disorder (ADHD) is a highly heterogeneous psychiatric disorder that can be divided into inattentive (I-ADHD), hyperactive-impulsive (HI-ADHD), and combined (C-ADHD) subtypes. Different early life events and environmental factors correlated with the gut microbiota community have been implicated in the development of ADHD. However, whether different ADHD symptomatic presentations are associated with distinct microbiota composition and function still unknown. Therefore, we carried out metagenomic analysis from 207 subjects to characterize the gut microbial profiles in ADHD and subgroup patients.ResultsThe current study revealed that the gut microbiota composition (beta diversity) can be effectively distinguished between C-ADHD patients and HCs, but not I-ADHD patients and HCs, nor general ADHD patients and HCs. Features include underrepresentation of 8 species belonging to the genus Bacteroides and enrichment of 5 species of Bifidobacterium and Prevotella in general ADHD patients (all p < 0.05). Eight of the above species became progressively reduced (ovatus, thetaiotaomicron, intestinalis, cellulosilyticus, and fluxus belonging to the genus Bacteroides) or enriched (Prevotella_copri, Prevotella_buccae and Bifidobacterium_breve) from healthy controls (HCs) to I-ADHD and C-ADHD patients. Predicted metabolic functions from these distinguished gut microbial markers described a certain compensatory host metabolism in ADHD and subgroup patients. Particularly, pyridoxal 5'-phosphate (a dominant vitamin B6 active type) biosynthesis pathways were significantly reduced in C-ADHD patients, because serum vitamin B6 deficiency in ADHD patients was found previously. Of note, we identified diverse virulence factor and antibiotic resistance from the gut microbiota of ADHD patients. The abundance of antibiotic resistance ontology ANT(9)-Ia positively correlated with the abundance of Prevotella_amnii, which was enriched in ADHD patients. Moreover, species-based bacterial markers were used to construct classifiers and achieved a higher AUC of 0.87 in C-ADHD vs. HC than that in ADHD vs. HC (AUC = 0.84).ConclusionsThese findings uncover alterations in microbial composition in subgroup patients and provide potential biomarkers for diagnosis different symptomatic presentations for ADHD.Trial registration: ClinicalTrials.gov, NCT03447223. Registered 27 February 2018, https://clinicaltrials.gov/ct2/show/NCT03447223?term=03447223&draw=2&rank=1

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Characterizing the Effects of Calcium and Prebiotic Fiber on Human Gut Microbiota Composition and Function Using a Randomized Crossover Design—A Feasibility Study

Nutrients ◽

10.3390/nu13061937 ◽

2021 ◽

Vol 13 (6) ◽

pp. 1937

Author(s):

Lara S. Yoon ◽

Karin B. Michels

Keyword(s):

Gut Microbiota ◽

Calcium Absorption ◽

Calcium Supplementation ◽

Random Sequence ◽

Human Study ◽

Crossover Design ◽

Microbiota Composition ◽

Microbial Composition ◽

And Function ◽

Prebiotic Fiber

Consumption of prebiotic inulin has been found to increase calcium absorption, which may protect against gut diseases such as colorectal cancer. This dietary relation may be modulated by compositional changes in the gut microbiota; however, no human study has addressed this hypothesis. We determined the feasibility of a randomized crossover trial to evaluate the effect of three interventions (combined calcium and inulin supplementation, calcium supplementation alone, and inulin supplementation alone) on the intestinal microbiota composition and function. We conducted a 16-week pilot study in 12 healthy adults who consumed the three interventions in a random sequence. Participants provided fecal and blood samples before and after each intervention. Each intervention period lasted four weeks and was flanked by one-week washout periods. 16S ribosomal RNA sequencing and quantification of short chain fatty acids (SCFA) was determined in fecal samples. Systemic lipopolysaccharide binding protein (LBP) was quantified in serum. Of the 12 individuals assigned to an intervention sequence, seven completed the study. Reasons for dropout included time (n = 3), gastrointestinal discomfort (n = 1), and moving (n = 1). Overall, participants reported positive attitudes towards the protocol (n = 9) but were unsatisfied by the practicalities of supplement consumption (44%) and experienced digestive discomfort (56%). We found no appreciable differences in microbial composition, SCFA concentration, nor LBP concentrations when comparing intervention periods. In conclusion, an intervention study using a randomized crossover design with calcium and a prebiotic fiber is feasible. Improvements of our study design include using a lower dose prebiotic fiber supplement and a larger sample size.

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Analysis of the developing gut microbiota in young dairy calves—impact of colostrum microbiota and gut disturbances

Tropical Animal Health and Production ◽

10.1007/s11250-020-02535-9 ◽

2020 ◽

Vol 53 (1) ◽

Author(s):

Bui Phan Thu Hang ◽

Ewa Wredle ◽

Johan Dicksved

Keyword(s):

Average Daily Gain ◽

Amplicon Sequencing ◽

Fecal Microbiota ◽

Dairy Calves ◽

Rrna Gene ◽

Microbiota Composition ◽

Microbial Composition ◽

Fecal Samples ◽

Calf Health ◽

Significant Difference

AbstractThe aim of this study was to characterize the colostrum and fecal microbiota in calves and to investigate whether fecal microbiota composition was related to colostrum microbiota or factors associated with calf health. Colostrum samples were collected in buckets after hand milking of 76 calving cows from 38 smallholder dairy farms. Fecal samples were taken directly from the rectum of 76 calves at birth and at 14 days age. The bacterial community structure in colostrum and feces was analyzed by terminal restriction fragment length polymorphism for all samples, and the microbial composition was determined by 16S rRNA gene amplicon sequencing for a subset of the samples (8 colostrum, 40 fecal samples). There was a significant difference in fecal microbiota composition between day 0 and day 14 samples, but no associations between the microbiota and average daily gain, birth weight, or transfer of passive immunity. At 14 days of age, Faecalibacterium and Butyricicoccus were prevalent in higher relative abundances in the gut of healthy calves compared to calves with diarrhea that had been treated with antimicrobials. Colostrum showed great variation in composition of microbiota but no association to fecal microbiota. This study provides the first insights into the composition of colostrum and fecal microbiota of young dairy calves in southern Vietnam and can form the basis for future more detailed studies.

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The Interplay between Mucosal Microbiota Composition and Host Gene-Expression is Linked with Infliximab Response in Inflammatory Bowel Diseases

Microorganisms ◽

10.3390/microorganisms8030438 ◽

2020 ◽

Vol 8 (3) ◽

pp. 438 ◽

Cited By ~ 5

Author(s):

Nikolas Dovrolis ◽

George Michalopoulos ◽

George E. Theodoropoulos ◽

Kostantinos Arvanitidis ◽

George Kolios ◽

...

Keyword(s):

Gene Expression ◽

16S Rrna Gene Sequencing ◽

Study Groups ◽

Rrna Gene ◽

Microbiota Composition ◽

Microbial Composition ◽

Patient Response ◽

Alpha And Beta Diversity ◽

Before And After ◽

Inflammatory Bowel

Even though anti-TNF therapy significantly improves the rates of remission in inflammatory bowel disease (IBD) patients, there is a noticeable subgroup of patients who do not respond to treatment. Dysbiosis emerges as a key factor in IBD pathogenesis. The aim of the present study is to profile changes in the gut microbiome and transcriptome before and after administration of the anti-TNF agent Infliximab (IFX) and investigate their potential to predict patient response to IFX at baseline. Mucosal biopsy samples from 20 IBD patients and nine healthy controls (HC) were examined for differences in microbiota composition (16S rRNA gene sequencing) and mucosal gene expression (RT-qPCR) at baseline and upon completion of IFX treatment, accordingly, via an in silico pipeline. Significant differences in microbiota composition were found between the IBD and HC groups. Several bacterial genera, which were found only in IBD patients and not HC, had their populations dramatically reduced after anti-TNF treatment regardless of response. Alpha and beta diversity metrics showed significant differences between our study groups. Correlation analysis revealed six microbial genera associated with differential expression of inflammation-associated genes in IFX treatment responders at baseline. This study shows that IFX treatment has a notable impact on both the gut microbial composition and the inflamed tissue transcriptome in IBD patients. Importantly, our results identify enterotypes that correlate with transcriptome changes and help differentiate IFX responders versus non-responders at baseline, suggesting that, in combination, these signatures can be an effective tool to predict anti-TNF response.

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PSIX-6 Gastrointestinal microbiome of calves fed solid diets containing different levels and sources of NDF

Journal of Animal Science ◽

10.1093/jas/skaa278.729 ◽

2020 ◽

Vol 98 (Supplement_4) ◽

pp. 418-419

Author(s):

Gercino F Virgínio Júnior ◽

Milaine Poczynek ◽

Ana Paula Silva ◽

Ariany Toledo ◽

Amanda Cezar ◽

...

Keyword(s):

Illumina Miseq ◽

Diversity Indices ◽

Dairy Calves ◽

Rrna Gene ◽

Gastrointestinal Microbiome ◽

Fecal Microbiome ◽

Miseq Platform ◽

Holstein Calves ◽

Ad Libitum ◽

Different Levels

Abstract Different levels and sources of NDF can modify the gastrointestinal microbiome. This study evaluated 18 Holstein calves housed in not-bedded suspended individual cages and fed one of three treatments: 22NDF - conventional starter containing 22% NDF (n = 7); 31NDF - starter with 31% NDF, replacing part of the corn by soybean hull (n = 6); and 22NDF+H - conventional starter with 22% NDF plus coast-cross hay ad libitum (n = 5). All animals received 4 L of milk replacer daily (24% CP; 18.5% fat; diluted to 12.5% solids), divided into two meals, being weaned at 8th week of age. After weaning, animals were housed in tropical shelters, fed with the respective solid diet and coast-cross hay ad libitum for all treatments. To evaluate the microbiome, ruminal fluid samples were collected using a modified Geishauser oral probe at weeks 2, 4, 6, 8 and 10, two hours after the morning feeding, and fecal samples were collected at birth (0) and at weeks 1, 2, 4, 8 and 10. The microbial community was determined by sequencing V3 and V4 region amplicons of the 16S rRNA gene that was amplified by PCR and sequenced by the Illumina MiSeq platform. Ruminal microbiome had no differences in diversity for the effects of weeks, treatments or interaction of both factors (Table 1). In feces, the diversity indices and evenness were higher for 22NDF+H when compared to 22NDF, with no difference for 31NDF. All indices were significantly affected by calves age. At birth, calves had the greatest diversity and richness. Week 1 and 2 had less evenness and diversity. Bacteroidota, Firmicutes_A and Firmicutes_C were the most abundant phylum in rumen and feces. The supply of hay was only effective in modifying the fecal microbiome of dairy calves, suggesting a resilience in the ruminal microbiome.

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Monitoring the variation in the gut microbiota of captive woolly monkeys related to changes in diet during a reintroduction process

Scientific Reports ◽

10.1038/s41598-021-85990-0 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Camilo Quiroga-González ◽

Luis Alberto Chica Cardenas ◽

Mónica Ramírez ◽

Alejandro Reyes ◽

Camila González ◽

...

Keyword(s):

Gut Microbiota ◽

Site Conditions ◽

Microbiota Composition ◽

Microbial Composition ◽

Bacterial Composition ◽

Diet Diversity ◽

Woolly Monkeys ◽

The Moment ◽

Positive Effect ◽

Lagothrix Lagothricha

AbstractMicrobiome is known to play an important role in the health of organisms and different factors such as diet have been associated with modifications in microbial communities. Differences in the microbiota composition of wild and captive animals has been evaluated; however, variation during a reintroduction process in primates has never been reported. Our aim was to identify changes in the bacterial composition of three individuals of reintroduced woolly monkeys (Lagothrix lagothricha) and the variables associated with such changes. Fecal samples were collected and the V4 region of the 16S rRNA gene was sequenced to determine gut microbial composition and functionality. Individual samples from released individuals showed a higher microbial diversity after being released compared to before liberation, associated with changes in their diet. Beta diversity and functionality analysis showed separation of samples from released and captive conditions and the major factor of variation was the moment of liberation. This study shows that intestinal microbiota varies depending on site conditions and is mainly associated with diet diversity. The intake of food from wild origin by released primates may promote a positive effect on gut microbiota, improving health, and potentially increasing success in reintroduction processes.

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Effects of long-acting, broad spectra anthelmintic treatments on the rumen microbial community compositions of grazing sheep

Scientific Reports ◽

10.1038/s41598-021-82815-y ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Christina D. Moon ◽

Luis Carvalho ◽

Michelle R. Kirk ◽

Alan F. McCulloch ◽

Sandra Kittelmann ◽

...

Keyword(s):

Archaeal Community ◽

Fungal Communities ◽

Control Group ◽

Microbiota Composition ◽

Rumen Microbiota ◽

Treatment Groups ◽

Methanobrevibacter Ruminantium ◽

Group 12 ◽

Relative Abundances ◽

Long Acting

AbstractAnthelmintic treatment of adult ewes is widely practiced to remove parasite burdens in the expectation of increased ruminant productivity. However, the broad activity spectra of many anthelmintic compounds raises the possibility of impacts on the rumen microbiota. To investigate this, 300 grazing ewes were allocated to treatment groups that included a 100-day controlled release capsule (CRC) containing albendazole and abamectin, a long-acting moxidectin injection (LAI), and a non-treated control group (CON). Rumen bacterial, archaeal and protozoal communities at day 0 were analysed to identify 36 sheep per treatment with similar starting compositions. Microbiota profiles, including those for the rumen fungi, were then generated for the selected sheep at days 0, 35 and 77. The CRC treatment significantly impacted the archaeal community, and was associated with increased relative abundances of Methanobrevibacter ruminantium, Methanosphaera sp. ISO3-F5, and Methanomassiliicoccaceae Group 12 sp. ISO4-H5 compared to the control group. In contrast, the LAI treatment increased the relative abundances of members of the Veillonellaceae and resulted in minor changes to the bacterial and fungal communities by day 77. Overall, the anthelmintic treatments resulted in few, but highly significant, changes to the rumen microbiota composition.

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