Gut microbiota composition does not associate with Toxoplasma infection in rats

Toxoplasma infection in intermediate host species closely associates with inflammation. This association has led to suggestions that the behavioural changes associated with infection may be indirectly driven by the resulting sustained inflammation rather than a direct behavioural manipulation by the parasite. If this is correct, sustained inflammation in chronically infected rodents should present as widespread changes in the gastrointestinal microbiota due to the dependency between the composition of these microbiota and sustained inflammation. We conducted a randomized controlled experiment in rats that were assigned to a Toxoplasma-treatment, placebo-treatment or negative control group. We sacrificed rats during the chronic phase of infection, collected their cecal stool samples and sequenced the V3-V4 region of the 16S rRNA gene to characterise the bacterial community in these samples. Toxoplasma infection did not induce widespread changes in the bacterial community composition of the gastrointestinal tract of rats. Rather, we found sex differences in the bacterial community composition and only minor changes in Toxoplasma infected rats. We conclude that it is unlikely that sustained inflammation is the mechanism driving the highly specific behavioural changes observed in Toxoplasma-positive rats.

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Exposure to Oxy-Tetracycline Changes Gut Bacterial Community Composition in Rainbow Trout: A Preliminary Study

Animals ◽

10.3390/ani11123404 ◽

2021 ◽

Vol 11 (12) ◽

pp. 3404

Author(s):

Aritra Roy Choudhury ◽

Ji-Young Park ◽

Do Young Kim ◽

Jeongyun Choi ◽

Satabdi Acharya ◽

...

Keyword(s):

Rainbow Trout ◽

Bacterial Community ◽

Community Composition ◽

Bacterial Community Composition ◽

Amplicon Sequencing ◽

Control Group ◽

Rrna Gene ◽

Scaling Analysis ◽

Treated Fish ◽

Aquaculture Management

The extensive use of antibiotics is evident in most of the livestock and aquaculture management for inhibiting pathogen infection. Korean aquaculture depends on the usage of oxy-tetracycline for growing rainbow trout. Hence, this study was conducted to evaluate the changes in gut bacterial community profiles of rainbow trout exposed to oxy-tetracycline and predict the metabolic functioning of the bacterial community. The gut bacterial community composition of oxy-tetracycline treated fish was assessed by amplicon sequencing targeting the 16S rRNA gene of bacteria and comparing with the control group that did not receive any antibiotic. The principle coordinate analysis and non-metric multidimensional scaling analysis had shown two distinct clusters that implies the changes in community composition. In phyla level, the relative abundances of Tenericutes and Firmicutes were observed to be significantly higher in oxy-tetracycline treated fish compared to the control. Furthermore, the prediction based metabolic profiling revealed the processes that are affected due to the shift in community profiles. For example, metabolic functioning of membrane efflux system, amino acid metabolism and glycolysis were significantly higher in oxy-tetracycline treated fish compared to the control. This study describes alteration in gut bacterial community composition and potential metabolic profiles of the community that might be responsible for surviving in antibiotic rich environment.

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Correlation of Breed, Growth Performance, and Rumen Microbiota in Two Rustic Cattle Breeds Reared Under Different Conditions

Frontiers in Microbiology ◽

10.3389/fmicb.2021.652031 ◽

2021 ◽

Vol 12 ◽

Author(s):

Matteo Daghio ◽

Francesca Ciucci ◽

Arianna Buccioni ◽

Alice Cappucci ◽

Laura Casarosa ◽

...

Keyword(s):

Bacterial Community ◽

Growth Performance ◽

Community Composition ◽

Lipid Composition ◽

High Throughput Sequencing ◽

Bacterial Community Composition ◽

Daily Weight Gain ◽

Rrna Gene ◽

Rumen Microbiota ◽

Cattle Breeds

The use of rustic cattle is desirable to face challenges brought on by climate change. Maremmana (MA) and Aubrac (AU) are rustic cattle breeds that can be successfully used for sustainable production. In this study, correlations between two rearing systems (feedlot and grazing) and the rumen microbiota, the lipid composition of rumen liquor (RL), and the growth performance of MA and AU steers were investigated. Bacterial community composition was characterized by high-throughput sequencing of 16S rRNA gene amplicons, and the RL lipid composition was determined by measuring fatty acid (FA) and the dimethyl acetal profiles. The main factor influencing bacterial community composition was the cattle breed. Some bacterial groups were positively correlated to average daily weight gain for the two breeds (i.e., Rikenellaceae RC9 gut group, Fibrobacter and Succiniclasticum in the rumen of MA steers, and Succinivibrionaceae UCG-002 in the rumen of AU steers); despite this, animal performance appeared to be influenced by short chain FAs production pathways and by the presence of H2 sinks that divert the H2 to processes alternative to the methanogenesis.

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Influence of host genetics in shaping the rumen bacterial community in beef cattle

Scientific Reports ◽

10.1038/s41598-020-72011-9 ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

Waseem Abbas ◽

Jeremy T. Howard ◽

Henry A. Paz ◽

Kristin E. Hales ◽

James E. Wells ◽

...

Keyword(s):

Bacterial Community ◽

Species Composition ◽

Community Composition ◽

Genetic Factors ◽

Bacterial Community Composition ◽

Gastrointestinal Microbiota ◽

Host Genetics ◽

A Genome ◽

Host Genetic ◽

Host Genetic Factors

Abstract In light of recent host-microbial association studies, a consensus is evolving that species composition of the gastrointestinal microbiota is a polygenic trait governed by interactions between host genetic factors and the environment. Here, we investigated the effect of host genetic factors in shaping the bacterial species composition in the rumen by performing a genome-wide association study. Using a common set of 61,974 single-nucleotide polymorphisms found in cattle genomes (n = 586) and corresponding rumen bacterial community composition, we identified operational taxonomic units (OTUs), Families and Phyla with high heritability. The top associations (1-Mb windows) were located on 7 chromosomes. These regions were associated with the rumen microbiota in multiple ways; some (chromosome 19; position 3.0–4.0 Mb) are associated with closely related taxa (Prevotellaceae, Paraprevotellaceae, and RF16), some (chromosome 27; position 3.0–4.0 Mb) are associated with distantly related taxa (Prevotellaceae, Fibrobacteraceae, RF16, RFP12, S24-7, Lentisphaerae, and Tenericutes) and others (chromosome 23; position 0.0–1.0) associated with both related and unrelated taxa. The annotated genes associated with identified genomic regions suggest the associations observed are directed toward selective absorption of volatile fatty acids from the rumen to increase energy availability to the host. This study demonstrates that host genetics affects rumen bacterial community composition.

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Dynamics of the bacterial community in a channel catfish nursery pond with a cage–pond integration system

Canadian Journal of Microbiology ◽

10.1139/cjm-2018-0268 ◽

2018 ◽

Vol 64 (12) ◽

pp. 954-967 ◽

Cited By ~ 2

Author(s):

Liqiang Zhong ◽

Daming Li ◽

Minghua Wang ◽

Xiaohui Chen ◽

Wenji Bian ◽

...

Keyword(s):

Bacterial Community ◽

16S Rrna ◽

16S Rrna Gene ◽

Community Composition ◽

Channel Catfish ◽

Bacterial Community Composition ◽

Rrna Gene ◽

Integration System ◽

Nursery Pond ◽

Site Variation

The changes in the bacterial community composition in a channel catfish nursery pond with a cage–pond integration system were investigated by sequencing of the 16S rRNA gene through Illumina MiSeq sequencing platforms. A total of 1 362 877 sequences and 1440 operational taxonomic units were obtained. Further analysis showed that the dominant phyla in the cage and pond groups were similar, including Actinobacteria, Cyanobacteria, Proteobacteria, and Bacteroidetes, although a significant difference was detected between them by ANOSIM (P < 0.05). Temporal changes and site variation were significantly related to the variation of the bacterial community. A comprehensive analysis of the diversity and evenness of the bacterial 16S rRNA gene, redundancy analysis (RDA), and partial Mantel test showed that the bacterial community composition in a cage–pond integration system was shaped more by temporal variation than by site variation. RDA also indicated that water temperature, total dissolved solids, and Secchi depth had the largest impact on bacterial populations.

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Bacterial community composition of a shallow hypertrophic freshwater lake in China, revealed by 16S rRNA gene sequences

FEMS Microbiology Ecology ◽

10.1111/j.1574-6941.2007.00326.x ◽

2007 ◽

Vol 61 (1) ◽

pp. 85-96 ◽

Cited By ~ 92

Author(s):

Xin Wu ◽

Wanyan Xi ◽

Wenjin Ye ◽

Hong Yang

Keyword(s):

Bacterial Community ◽

16S Rrna ◽

16S Rrna Gene ◽

Community Composition ◽

Bacterial Community Composition ◽

Freshwater Lake ◽

Rrna Gene ◽

Gene Sequences ◽

16S Rrna Gene Sequences

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Gut bacterial communities across 12 Ensifera (Orthoptera) at different feeding habits and its prediction for the insect with contrasting feeding habits

PLoS ONE ◽

10.1371/journal.pone.0250675 ◽

2021 ◽

Vol 16 (4) ◽

pp. e0250675

Author(s):

Xiang Zheng ◽

Qidi Zhu ◽

Zhijun Zhou ◽

Fangtong Wu ◽

Lixuan Chen ◽

...

Keyword(s):

Community Structure ◽

Bacterial Community ◽

Community Composition ◽

Bacterial Community Structure ◽

Feeding Habits ◽

Bacterial Community Composition ◽

Critical Role ◽

Taxonomic Status ◽

Rrna Gene ◽

Insect Gut

Insect microbial symbioses play a critical role in insect lifecycle, and insect gut microbiome could be influenced by many factors. Studies have shown that host diet and taxonomy have a strong influence on insect gut microbial community. In this study, we performed sequencing of V3-V4 region of 16S rRNA gene to compare the composition and diversity of 12 Ensifera from 6 provinces of China. Moreover, the influences of feeding habits and taxonomic status of insects on their gut bacterial community were evaluated, which might provide reference for further application research. The results showed that Proteobacteria (45.66%), Firmicutes (34.25%) and Cyanobacteria (7.7%) were the predominant bacterial phyla in Ensifera. Moreover, the gut bacterial community composition of samples with different feeding habits was significantly different, which was irrespective of their taxa. The highest diversity of gut bacteria was found in the omnivorous Ensifera. Furthermore, common and unique bacteria with biomarkers were found based on the dietary characteristics of the samples. However, the bacterial community structure of the Ensifera samples was significantly different from that of Caelifera. Therefore, we concluded that feeding habits and taxonomic status jointly affect the gut bacterial community composition of the samples from Orthoptera. However, the influence of feeding habit dominates when taxonomy category below the suborder level. In addition, the dominant, common and unique bacterial community structure could be used to predict the contrastic feeding habits of insects belonging to Ensifera.

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Assessing the microbiota of recycled bedding sand on a Wisconsin dairy farm

Journal of Animal Science and Biotechnology ◽

10.1186/s40104-021-00635-6 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Hannah E. Pilch ◽

Andrew J. Steinberger ◽

Donald C. Sockett ◽

Nicole Aulik ◽

Garret Suen ◽

...

Keyword(s):

Bacterial Community ◽

Community Composition ◽

Pathogenic Bacteria ◽

Bacterial Community Composition ◽

Dairy Farm ◽

Amplicon Sequencing ◽

Rrna Gene ◽

Recycling System ◽

Core Microbiota ◽

Relative Abundances

Abstract Background Sand is often considered the preferred bedding material for dairy cows as it is thought to have lower bacterial counts than organic bedding materials and cows bedded on sand experience fewer cases of lameness and disease. Sand can also be efficiently recycled and reused, making it cost-effective. However, some studies have suggested that the residual organic material present in recycled sand can serve as a reservoir for commensal and pathogenic bacteria, although no studies have yet characterized the total bacterial community composition. Here we sought to characterize the bacterial community composition of a Wisconsin dairy farm bedding sand recycling system and its dynamics across several stages of the recycling process during both summer and winter using 16S rRNA gene amplicon sequencing. Results Bacterial community compositions of the sand recycling system differed by both seasons and stage. Summer samples had higher richness and distinct community compositions, relative to winter samples. In both summer and winter samples, the diversity of recycled sand decreased with time drying in the recycling room. Compositionally, summer sand 14 d post-recycling was enriched in operational taxonomic units (OTUs) belonging to the genera Acinetobacter and Pseudomonas, relative to freshly washed sand and sand from cow pens. In contrast, no OTUs were found to be enriched in winter sand. The sand recycling system contained an overall core microbiota of 141 OTUs representing 68.45% ± 10.33% SD of the total bacterial relative abundance at each sampled stage. The 4 most abundant genera in this core microbiota included Acinetobacter, Psychrobacter, Corynebacterium, and Pseudomonas. Acinetobacter was present in greater abundance in summer samples, whereas Psychrobacter and Corynebacterium had higher relative abundances in winter samples. Pseudomonas had consistent relative abundances across both seasons. Conclusions These findings highlight the potential of recycled bedding sand as a bacterial reservoir that warrants further study.

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Vaginal bacterial community composition and concentrations of estradiol at the time of artificial insemination in Brangus heifers

Journal of Animal Science ◽

10.1093/jas/skaa178 ◽

2020 ◽

Vol 98 (6) ◽

Cited By ~ 1

Author(s):

Riley D Messman ◽

Zully E Contreras-Correa ◽

Henry A Paz ◽

George Perry ◽

Caleb O Lemley

Keyword(s):

Bacterial Community ◽

Community Composition ◽

Artificial Insemination ◽

Beta Diversity ◽

Bacterial Community Composition ◽

Alpha Diversity ◽

Species Level ◽

Rrna Gene ◽

Microbial Composition ◽

Vaginal Tract

Abstract The knowledge surrounding the bovine vaginal microbiota and its implications on fertility and reproductive traits remains incomplete. The objective of the current study was to characterize the bovine vaginal bacterial community and estradiol concentrations at the time of artificial insemination (AI). Brangus heifers (n = 78) underwent a 7-d Co-Synch + controlled internal drug release estrus synchronization protocol. At AI, a double-guarded uterine culture swab was used to sample the anterior vaginal tract. Immediately after swabbing the vaginal tract, blood samples were collected by coccygeal venipuncture to determine concentrations of estradiol. Heifers were retrospectively classified as pregnant (n = 29) vs. nonpregnant (n = 49) between 41 and 57 d post-AI. Additionally, heifers were classified into low (1.1 to 2.5 pg/mL; n = 21), medium (2.6 to 6.7 pg/mL; n = 30), and high (7.2 to 17.6 pg/mL; n = 27) concentration of estradiol. The vaginal bacterial community composition was determined through sequencing of the V4 region from the 16S rRNA gene using the Illumina Miseq platform. Alpha diversity was compared via ANOVA and beta diversity was compared via PERMANOVA. There were no differences in the Shannon diversity index (alpha diversity; P = 0.336) or Bray–Curtis dissimilarity (beta diversity; P = 0.744) of pregnant vs. nonpregnant heifers. Overall, bacterial community composition in heifers with high, medium, or low concentrations of estradiol did not differ (P = 0.512). While no overall compositional differences were observed, species-level differences were present within pregnancy status and estradiol concentration groups. The implications of these species-level differences are unknown, but these differences could alter the vaginal environment thereby influencing fertility and vaginal health. Therefore, species-level changes could provide better insight rather than overall microbial composition in relation to an animal’s reproductive health.

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Ruminal Bacterial Community Composition in Dairy Cows Is Dynamic over the Course of Two Lactations and Correlates with Feed Efficiency

Applied and Environmental Microbiology ◽

10.1128/aem.00720-15 ◽

2015 ◽

Vol 81 (14) ◽

pp. 4697-4710 ◽

Cited By ~ 112

Author(s):

Kelsea A. Jewell ◽

Caroline A. McCormick ◽

Christine L. Odt ◽

Paul J. Weimer ◽

Garret Suen

Keyword(s):

Bacterial Community ◽

Community Composition ◽

Milk Production ◽

Feed Efficiency ◽

Production Efficiency ◽

Bacterial Community Composition ◽

Feed Consumption ◽

Rrna Gene ◽

Content Type ◽

Bacterial Microbiota

ABSTRACTFourteen Holstein cows of similar ages were monitored through their first two lactation cycles, during which ruminal solids and liquids, milk samples, production data, and feed consumption data were collected for each cow during early (76 to 82 days in milk [DIM]), middle (151 to 157 DIM), and late (251 to 257 DIM) lactation periods. The bacterial community of each ruminal sample was determined by sequencing the region from V6 to V8 of the 16S rRNA gene using 454 pyrosequencing. Gross feed efficiency (GFE) for each cow was calculated by dividing her energy-corrected milk by dry matter intake (ECM/DMI) for each period of both lactation cycles. Four pairs of cows were identified that differed in milk production efficiency, as defined by residual feed intake (RFI), at the same level of ECM production. The most abundant phyla detected for all cows wereBacteroidetes(49.42%),Firmicutes(39.32%),Proteobacteria(5.67%), andTenericutes(2.17%), and the most abundant genera includedPrevotella(40.15%),Butyrivibrio(2.38%),Ruminococcus(2.35%),Coprococcus(2.29%), andSucciniclasticum(2.28%). The bacterial microbiota between the first and second lactation cycles were highly similar, but with a significant correlation between total community composition by ruminal phase and specific bacteria whose relative sequence abundances displayed significant positive or negative correlation with GFE or RFI. These data suggest that the ruminal bacterial community is dynamic in terms of membership and diversity and that specific members are associated with high and low milk production efficiency over two lactation cycles.

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