scholarly journals Temporal Dynamics in Rumen Bacterial Community Composition of Finishing Steers during an Adaptation Period of Three Months

2019 ◽  
Vol 7 (10) ◽  
pp. 410 ◽  
Author(s):  
Qinghua Qiu ◽  
Chaoyu Gao ◽  
Zhibiao Gao ◽  
Muhammad Aziz ur Rahman ◽  
Yang He ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Community Composition ◽  
Relative Abundance ◽  
Temporal Dynamics ◽  
Bacterial Community Composition ◽  
Rrna Gene ◽  
Adaptation Period ◽  
Finishing Steers ◽  
Sampling Intervals ◽  
Dietary Treatments

The objective of this study was to explore whether collecting rumen samples of finishing steers at monthly intervals differed, and whether this difference or similarity varied with diets. For these purposes, 12 Chinese Holstein steers were equally divided into two groups. The dietary treatments were either standard energy and standard protein (C) or low energy and low protein (L). Rumen samples were obtained on day 30, day 60 and day 90 from both dietary treatments and were analyzed by using 16S rRNA gene sequencing. The results showed that monthly intervals had no effect on the richness and evenness of the rumen bacterial community in the two diets. However, taxonomic difference analysis (relative abundance >0.5%) revealed that the relative abundance of three phyla (Proteobacteria, Fibrobacteres and Cyanobacteria) and six genera (Rikenellaceae_RC9_gut_group, Ruminococcaceae_NK4A214_group, Fibrobacter, Eubacterium_coprostanoligenes_group, Ruminococcaceae_UCG-010 and Ruminobacter) were significantly different between monthly sampling intervals, and the difference was prominent between sampling in the first month and the subsequent two months. Moreover, the differences in abundances of phyla and genera between monthly sampling intervals were affected by diets. Analysis of similarity (ANOSIM) showed no significant differences between monthly sampling intervals in the C diet. However, ANOSIM results revealed that significant differences between the first month and second month and between the first month and third month were present in the L diet. These results indicated that temporal dynamics in rumen bacterial community composition did occur even after an adaptation period of three months. This study tracked the changes in rumen bacterial populations of finishing cattle after a shift in diet with the passage of time. This study may provide insight into bacterial adaptation time to dietary transition in finishing steers.

scholarly journals Habitual Sleep Duration and the Colonic Mucosa-Associated Gut Microbiota in Humans—A Pilot Study

2021 ◽  
Vol 3 (3) ◽  
pp. 387-397
Author(s):  
Ritwick Agrawal ◽  
Nadim J. Ajami ◽  
Sonal Malhotra ◽  
Liang Chen ◽  
Donna L. White ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Gut Microbiota ◽  
Sleep Duration ◽  
Community Composition ◽  
Relative Abundance ◽  
Bacterial Community Composition ◽  
Multivariable Analysis ◽  
Rrna Gene ◽  
Sleep Habits ◽  
Nocturnal Sleep

We examined the association between the colonic adherent microbiota and nocturnal sleep duration in humans. In a cross-sectional study, 63 polyp-free adults underwent a colonoscopy and donated 206 mucosal biopsies. The gut microbiota was profiled using the 16S rRNA gene sequencing targeting the V4 region. The sequence reads were processed using UPARSE and DADA2, respectively. Lifestyle factors, including sleep habits, were obtained using an interviewer-administered questionnaire. We categorized the participants into short sleepers (<6 h per night; n = 16) and normal sleepers (6–8 h per night; n = 47) based on self-reported data. Differences in bacterial biodiversity and the taxonomic relative abundance were compared between short vs. normal sleepers, followed by multivariable analysis. A false discovery rate-adjusted p value (q value) < 0.05 indicated statistical significance. The bacterial community composition differed in short and normal sleepers. The relative abundance of Sutterella was significantly lower (0.38% vs. 1.25%) and that of Pseudomonas was significantly higher (0.14% vs. 0.08%) in short sleepers than in normal sleepers (q values < 0.01). The difference was confirmed in the multivariable analysis. Nocturnal sleep duration was associated with the bacterial community composition and structure in the colonic gut microbiota in adults.

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

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.

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

2018 ◽  
Vol 64 (12) ◽  
pp. 954-967 ◽  
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.

scholarly journals Impact of Biochar Application to Soil on the Root-Associated Bacterial Community Structure of Fully Developed Greenhouse Pepper Plants

2011 ◽  
Vol 77 (14) ◽  
pp. 4924-4930 ◽  
Author(s):  
Max Kolton ◽  
Yael Meller Harel ◽  
Zohar Pasternak ◽  
Ellen R. Graber ◽  
Yigal Elad ◽  
...  
Keyword(s):  
Bacterial Community ◽  
16S Rrna ◽  
Relative Abundance ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Bacterial Community Composition ◽  
Systemic Resistance ◽  
Rrna Gene ◽  
Molecular Fingerprinting ◽  
Content Type ◽  
Biochar Amendment

ABSTRACTAdding biochar to soil has environmental and agricultural potential due to its long-term carbon sequestration capacity and its ability to improve crop productivity. Recent studies have demonstrated that soil-applied biochar promotes the systemic resistance of plants to several prominent foliar pathogens. One potential mechanism for this phenomenon is root-associated microbial elicitors whose presence is somehow augmented in the biochar-amended soils. The objective of this study was to assess the effect of biochar amendment on the root-associated bacterial community composition of mature sweet pepper (Capsicum annuumL.) plants. Molecular fingerprinting (denaturing gradient gel electrophoresis and terminal restriction fragment length polymorphism) of 16S rRNA gene fragments showed a clear differentiation between the root-associated bacterial community structures of biochar-amended and control plants. The pyrosequencing of 16S rRNA amplicons from the rhizoplane of both treatments generated a total of 20,142 sequences, 92 to 95% of which were affiliated with theProteobacteria,Bacteroidetes,Actinobacteria, andFirmicutesphyla. The relative abundance of members of theBacteroidetesphylum increased from 12 to 30% as a result of biochar amendment, while that of theProteobacteriadecreased from 71 to 47%. TheBacteroidetes-affiliatedFlavobacteriumwas the strongest biochar-induced genus. The relative abundance of this group increased from 4.2% of total root-associated operational taxonomic units (OTUs) in control samples to 19.6% in biochar-amended samples. Additional biochar-induced genera included chitin and cellulose degraders (ChitinophagaandCellvibrio, respectively) and aromatic compound degraders (HydrogenophagaandDechloromonas). We hypothesize that these biochar-augmented genera may be at least partially responsible for the beneficial effect of biochar amendment on plant growth and viability.

scholarly journals Temporal Dynamics of South End Tidal Creek (Sapelo Island, Georgia) Bacterial Communities

2008 ◽  
Vol 75 (4) ◽  
pp. 1058-1064 ◽  
Author(s):  
Emily Kara ◽  
Ashley Shade
Keyword(s):  
Bacterial Community ◽  
Community Composition ◽  
Community Dynamics ◽  
Tidal Creek ◽  
Temporal Dynamics ◽  
Bacterial Community Composition ◽  
High Tide ◽  
Cycle Period ◽  
Sapelo Island ◽  
End Tidal

ABSTRACT Bacterial community dynamics in South End tidal creek, Sapelo Island, GA, were studied over a 74-h, five-tidal-cycle period. Observations were made hourly for the first consecutive 24 hours, every 3 hours on the second day, and every 6 hours on the third day. Tide most strongly influenced bacterial community composition (high-tide versus low-tide community analysis of similarities, R = 0.41, P < 0.03). Dissolved oxygen concentration and conductivity were important proximate drivers. However, after accounting for tide and environmental variables colinear with tide, cumulative time became more important in describing community variation. In-stream physical processes, including particulate suspension and sedimentation, may explain tide-associated trends in the bacterial community composition observed.

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

PLoS ONE ◽  
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.

scholarly journals Gut microbiota composition does not associate with Toxoplasma infection in rats

2021 ◽  
Author(s):  
Patrick Taggart ◽  
Craig Liddicoat ◽  
Wen Han Tong ◽  
Martin Breed ◽  
Philip Weinstein ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Community Composition ◽  
Bacterial Community Composition ◽  
Chronic Phase ◽  
Negative Control ◽  
Control Group ◽  
Rrna Gene ◽  
Gastrointestinal Microbiota ◽  
Toxoplasma Infection ◽  
Behavioural Changes

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.

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

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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