scholarly journals The Temporal Dynamics of Rumen Microbiota in Early Weaned Lambs

2022 ◽  
Vol 10 (1) ◽  
pp. 144
Author(s):  
Shiqin Wang ◽  
Jianmin Chai ◽  
Guohong Zhao ◽  
Naifeng Zhang ◽  
Kai Cui ◽  
...  
Keyword(s):  
Temporal Dynamics ◽  
Early Weaning ◽  
Ruminal Bacteria ◽  
Linear Discriminant ◽  
Rumen Microbiota ◽  
Weaning Stress ◽  
Short Period ◽  
Relative Abundances ◽  
Abundance And Diversity ◽  
Generation Sequencing

Weaning affects the development of ruminal bacteria in lambs during early life. However, the temporal dynamics of rumen microbiota in early weaned lambs is unknown compared to conventionally weaned lambs. In this study, one group was reared with their dams (control, CON) and conventionally weaned at 49 days (d), while the other lambs were weaned at 21 d (early weaning, EW) using starter. Rumen microbial samples collected at 26, 35, and 63 d were used for next-generation sequencing. Here, we found that the abundance and diversity of rumen microbiota in EW were significantly lower at 26 and 35 d than the CON. Linear discriminant analysis Effect Size (LEfSe) analysis was performed to identify the signature microbiota for EW at these three ages. At 26 d, Prevotella 7, Syntrophococcus, Sharpea, Dialister, Pseudoscardovia, and Megasphaera in the rumen of the EW group had greater relative abundances. At 35 d, the Lachnospiraceae_NK3A20_group was enriched in CON. On 63 d, Erysipelotrichaceae_UCG-002 was abundant in EW. Syntrophococcus and Megaspheaera in EW lambs were abundant at 26 and 35 d, but kept similar to CON at 63 d. The relative abundance of Erysipelotrichaceae_UCG-002 at all-time points was consistently higher in the EW group. In conclusion, early weaning led to a significant decrease in rumen microbiota richness and diversity in the short term. The changes in rumen microbiota are associated with the persistence of weaning stress. The temporal dynamics of relative abundances of Syntrophococcus, Megasphaera, and Ruminococcaceae_UCG-014 reflect the weaning stress over a short period and rumen recovery after early weaning.

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

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.

scholarly journals Variations in the Community Structure of Fungal Microbiota Associated with Apple Fruit Shaped by Fruit Bagging-Based Practice

2021 ◽  
Vol 7 (9) ◽  
pp. 764
Author(s):  
Punda Khwantongyim ◽  
Somying Wansee ◽  
Xi Lu ◽  
Wei Zhang ◽  
Guangyu Sun
Keyword(s):  
Management Practice ◽  
Agricultural Practices ◽  
Apple Fruit ◽  
Fungal Communities ◽  
Compositional Variation ◽  
Fungal Microbiota ◽  
Abundance And Diversity ◽  
Generation Sequencing ◽  
Fruit Part ◽  
Fruit Bagging

The various fungal communities that adhere to apple fruit are influenced by agricultural practices. However, the effects of fruit bagging-based management practice on the fungal microbiota are still unknown, and little is known about the fungal communities of bagged apple fruit. We conducted a study using apple fruit grown in a conventionally managed orchard where pesticide use is an indispensable practice. Fungal communities were collected from the calyx-end and peel tissues of bagged and unbagged fruit and characterized using barcode-type next-generation sequencing. Fruit bagging had a stronger effect on fungal richness, abundance, and diversity of the fungal microbiota in comparison to non-bagging. In addition, bagging also impacted the compositional variation of the fungal communities inhabiting each fruit part. We observed that fruit bagging had a tendency to maintain ecological equilibrium since Ascomycota and Basidiomycota were more distributed in bagged fruit than in unbagged fruit. These fungal communities consist of beneficial fungi rather than potentially harmful fungi. Approximately 50 dominant taxa were detected in bagged fruit, for example, beneficial genera such as Articulospora, Bullera, Cryptococcus, Dioszegia, Erythrobasidium, and Sporobolomyces, as well as pathogenic genera such as Aureobasidium and Taphrina. These results suggested that fruit bagging could significantly increase fungal richness and promote healthy fungal communities, especially the harmless fungal communities, which might be helpful for protecting fruit from the effects of pathogens. This study provides a foundation for understanding the impacts of bagging-based practice on the associated fungal microbiota.

scholarly journals Metatranscriptomic Analysis of Sub-Acute Ruminal Acidosis in Beef Cattle

Animals ◽  
2019 ◽  
Vol 9 (5) ◽  
pp. 232 ◽  
Author(s):  
Ibukun Ogunade ◽  
Andres Pech-Cervantes ◽  
Hank Schweickart
Keyword(s):  
Beef Cattle ◽  
Rumen Fluid ◽  
Control Diet ◽  
Bacterial Biofilm ◽  
Ruminal Bacteria ◽  
Subacute Ruminal Acidosis ◽  
Rumen Microbiota ◽  
Ruminal Acidosis ◽  
Rrna Sequencing ◽  
Illumina Hiseq4000

Subacute ruminal acidosis (SARA) is a metabolic disease of ruminants characterized by low pH, with significant impacts on rumen microbial activity, and animal productivity and health. Microbial changes during subacute ruminal acidosis have previously been analyzed using quantitative PCR and 16S rRNA sequencing, which do not reveal the actual activity of the rumen microbial population. Here, we report the functional activity of the rumen microbiota during subacute ruminal acidosis. Eight rumen-cannulated Holstein steers were assigned randomly to acidosis-inducing or control diet. Rumen fluid samples were taken at 0, 3, 6, and 9 h relative to feeding from both treatments on the challenge day. A metatranscriptome library was prepared from RNA extracted from the samples and the sequencing of the metatranscriptome library was performed on Illumina HiSeq4000 following a 2 × 150 bp index run. Cellulolytic ruminal bacteria including Fibrobacter succinogenes, Ruminococcus albus, and R. bicirculans were reduced by an induced acidotic challenge. Up to 68 functional genes were differentially expressed between the two treatments. Genes mapped to carbohydrate, amino acid, energy, vitamin and co-factor metabolism pathways, and bacterial biofilm formation pathways were enriched in beef cattle challenged with sub-acute acidosis. This study reveals transcriptionally active taxa and metabolic pathways of rumen microbiota during induced acidotic challenge.

Effect of early weaning at about 30 days after farrowing on the reproductive characteristics in gilts and sows

1969 ◽  
Vol 72 (2) ◽  
pp. 247-250 ◽  
Author(s):  
Hirokazu Shimizu ◽  
Saburo Takeuchi
Keyword(s):  
Seasonal Changes ◽  
Average Weight ◽  
Early Weaning ◽  
Reproductive Characteristics ◽  
Short Period ◽  
Heat Period

SUMMARYRecords have been analysed from a small herd in which early weaning was practised. Piglets were weaned when average weight was 7–8 kg, at about 30 days old. Decreased feeding of sows, followed by a short period of fasting, was practised at weaning.Mean duration of suckling was 31·5 days and mean interval from weaning to oestrus 6·0 days. 93% of sows conceived to service at the first or second heat period. Mean farrowing interval for all sows was 159·7 days (151·9 days for those holding to the first service). Corresponding annual farrowing frequencies, calculated from these figures, are 2·29 and 2·40.Litter sizes at birth and at weaning were 10·7 and 9·3; corresponding weights of piglets were 1·74 and 7·99 kg. With increase of litter sequence there was a significant decrease of weaning weights; however, there was also an increase in size of litter weaned. Seasonal changes of piglet weight were also found. Early weaning can be considered a useful way to increase production.

scholarly journals Alcov: Estimating Variant of Concern Abundance from SARS-CoV-2 Wastewater Sequencing Data

2021 ◽  
Author(s):  
Isaac Ellmen ◽  
Michael D.J. Lynch ◽  
Delaney Nash ◽  
Jiujun Cheng ◽  
Jozef I. Nissimov ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Clinical Data ◽  
Relative Abundance ◽  
Community Level ◽  
Next Generation ◽  
Sequencing Data ◽  
Complete Genomes ◽  
Relative Abundances ◽  
Wastewater Samples ◽  
Generation Sequencing

Detection of SARS-CoV-2 in wastewater is an important strategy for community level surveillance. Variants of concern (VOCs) can be detected in the wastewater samples using next generation sequencing, however it can be challenging to determine the relative abundance of different VOCs since the reads cannot be assembled into complete genomes. Here, we present Alcov (abundance learning of SARS-CoV-2 variants), a tool that uses mutation frequencies in SARS-CoV-2 sequencing data to predict the distribution of VOC lineages in the sample. We used Alcov to predict the distributions of lineages from three wastewater samples which agreed well with clinical data. By predicting not just which VOCs are present, but their relative abundances in the population, Alcov extracts a more complete snapshot of the variants which are circulating in a community.

scholarly journals Paired-end small RNA sequencing reveals a possible overestimation in the isomiR sequence repertoire previously reported from conventional single read data analysis

2021 ◽  
Author(s):  
Jose Francisco Sanchez-Herrero ◽  
Raquel Pluvinet ◽  
Antonio Luna-de Haro ◽  
Lauro Sumoy
Keyword(s):  
Data Analysis ◽  
Rna Sequencing ◽  
Small Rna ◽  
Small Rna Sequencing ◽  
Sequencing Data ◽  
Technical Noise ◽  
Sequencing Errors ◽  
Abundance And Diversity ◽  
Template Dna ◽  
Generation Sequencing

Abstract Background Next generation sequencing has allowed the discovery of miRNA isoforms, termed isomirs. Some isomirs are derived from imprecise processing of pre-miRNA precursors, leading to length variants. Additional variability is introduced by non-templated addition of bases at the ends or editing of internal bases, resulting in base differences relative to the template DNA sequence. We hypothesized that some component of the isomir variation reported so far could be due to systematic technical noise and not real. Results We have developed the XICRA pipeline to analyze small RNA sequencing data at the isomir level. We exploited its ability to use single or merged reads to compare isomir results derived from paired-end (PE) reads with those from single reads (SR) to address whether detectable sequence differences relative to canonical miRNAs found in isomirs are true biological variations or the result of errors in sequencing. We have detected non-negligible systematic differences between SR and PE data which primarily affect putative internally edited isomirs, and at a much smaller frequency terminal length changing isomirs. This is relevant for the identification of true isomirs in small RNA sequencing datasets. Conclusions We conclude that potential artifacts derived from sequencing errors and/or data processing could result in an overestimation of abundance and diversity of miRNA isoforms. Efforts in annotating the isomirnome should take this into account.

scholarly journals Diet dominates age in shaping the rumen bacteria community and function in dairy cattle

2021 ◽  
Author(s):  
Yangyi Hao ◽  
Yue Gong ◽  
Shuai Huang ◽  
Shoukun Ji ◽  
Wei Wang ◽  
...  
Keyword(s):  
Dairy Cattle ◽  
Rumen Fluid ◽  
Variation Partitioning ◽  
Rumen Bacteria ◽  
Ruminal Bacteria ◽  
Linear Discriminant ◽  
High Fiber ◽  
Fiber Diet ◽  
Α Diversity ◽  
And Function

Abstract Background To understand the effects of diet and age on the rumen bacterial community and function, forty-eight dairy cattle at 1.5 (M1.5), 6 (M6), 9 (M9), 18 (M18), 23 (M23), and 27 (M27) months old were selected. The M1.5, M6, and M27 had the high protein and starch dietary, while the M9, M18, and M23 had the high fiber dietary. Fermentation profile, enzyme activity, and bacteria community in rumen fluid were measured. Results The acetate to propionate ratio (A/P) at M9, M18, and M23 (high fiber diet) was higher than other ages, and M6 was the lowest (P < 0.05). The total volatile fatty acid (TVFA) at M23 and M27 was higher than other ages (P < 0.05). The urease at M18 was lower than M1.5, M6, and M9, and the xylanase at M18 was higher than M1.5, M23, and M27 (P < 0.05). The α-diversity indexes (Ace and Chao1) of ruminal bacteria increased from M1.5 to M23, while they decreased from M23 to M27 (P < 0.05). Thirty-three bacteria were identified as biomarkers of the different groups based on the linear discriminant analysis (LDA) when the LDA score > 4. The variation partitioning approach analysis showed that the age and diet had a 7.98% and 32.49% contribution to the rumen bacteria community variation, respectively. The richness of Succinivibrionaceae_UCG-002 and Fibrobacter were positive correlated with age (r > 0.60, P < 0.01) and also positively correlated with TVFA and acetate (r > 0.50, P < 0.01). The Lachnospiraceae_AC2044_group, Pseudobutyrivibrio, and Saccharofermentans has a positive correlation (r > 0.80, P < 0.05) with diet NDF and negative correlation (r < -0.80, P < 0.05) with diet CP and starch, which were also positively correlated with the acetate and A/P (r > 0.50, P < 0.01). Conclusion These findings indicated that the quantitative effect of diet and age on the rumen bacteria were 7.98% and 32.49%, respectively. The genera of Lachnospiraceae_AC2044_group, Pseudobutyrivibrio, and Saccharofermentans could be worked as the target bacteria to modulate the rumen fermentation by diet; meanwhile, the high age-correlated bacteria such as Succinivibrionaceae_UCG-002 and Fibrobacter also should be considered when shaping the rumen function.

scholarly journals Multivariate statistical techniques for metagenomic analysis of microbial community recovered from environmental samples

2018 ◽  
Vol 24 ◽  
pp. 45-53 ◽  
Author(s):  
Z Akond ◽  
M Alam ◽  
MS Ahmed ◽  
MNH Mollah
Keyword(s):  
Microbial Communities ◽  
Microbial Mats ◽  
Statistical Techniques ◽  
Multivariate Statistical ◽  
Linear Discriminant ◽  
Metabolic Functions ◽  
Metabolic Variables ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing ◽  
Shed Light

High-throughput big dataset generated through next generation sequencing (NGS) of DNA samples helps identify key differences in the function and taxonomy between microbial communities as well as shed light on the diversity of microbes, cooperation and evolution in any particular ecosystem. During this study, three statistical techniques namely, Random Forest (RF), Multidimensional Scaling (MDS) and Linear Discriminant Analysis (LDA) approaches were employed for functional analysis of 212 publicly available metagenomic datasets within and between 10 environments against 27 metabolic functions. RF generates the 8 most important metabolic variables along with MDS and LDA among which Photosynthesis has the highest score (70.20); Phages, prophages has the second highest score (61.31) and Membrane Transport was found to have the eighth highest score (45.29). The MDS plot was found useful to visualize the separation of the microbes from human or animal hosts from other samples along the first dimension and the separation of the aquatic and mat communities along the second dimension. LDA analyses compared the extent of the microbial samples into three broad groups: the human and animal associated samples, the microbial mats, and the aquatic samples. RF showed that phage activity is a major difference between host-associated microbial communities and free-living. The MDS and LDA techniques suggest that mat communities were unique from both the animal associated metagenomes and the aquatic samples with differences in the vitamin and cofactor metabolism.J. bio-sci. 24: 45-53, 2016

scholarly journals Dietary Supplementation with Sodium Sulfate Improves Rumen Fermentation, Fiber Digestibility, and the Plasma Metabolome through Modulation of Rumen Bacterial Communities in Steers

2020 ◽  
Vol 86 (22) ◽  
Author(s):  
Yuchao Zhao ◽  
Biao Xie ◽  
Jian Gao ◽  
Guangyong Zhao
Keyword(s):  
Amino Acids ◽  
Sodium Sulfate ◽  
Dietary Supplementation ◽  
Rumen Fermentation ◽  
Purine Derivatives ◽  
Rumen Microbiota ◽  
Fiber Digestibility ◽  
Plasma Metabolome ◽  
Relative Abundances ◽  
Present Trial

ABSTRACT Six steers were used to study the effects of dietary supplementation with sodium sulfate (Na2SO4) on rumen fermentation, nutrient digestion, rumen microbiota, and plasma metabolites. The animals were fed a basal ration with Na2SO4 added at 0 g/day (sulfur [S] content of 0.115% dry matter [DM]), 20 g/day (S at 0.185% DM), or 40 g/day (S at 0.255% DM) in a replicate 3-by-3 Latin square design. The results indicated that supplementing with Na2SO4 increased the ruminal concentration of total volatile fatty acids, the molar proportions of acetate and butyrate, the ruminal concentrations of microbial protein, SO42−-S, and S2−-S, and the digestibility of fiber, while it decreased the molar proportion of propionate and the ruminal concentration of ammonia nitrogen. Supplementing with Na2SO4 increased the diversity and the richness of rumen microbiota and the relative abundances of the phylum Firmicutes and genera Ruminococcus 2, Rikenellaceae RC9 gut group, and Desulfovibrio, whereas it decreased the relative abundances of the phylum Bacteroidetes and genera Prevotella 1, Prevotellaceae UCG-001, and Treponema 2. Supplementing with Na2SO4 also increased the plasma concentrations of amino acids (l-arginine, l-methionine, l-cysteine, and l-lysine), purine derivatives (xanthine and hypoxanthine), vitamins (thiamine and biotin), and lipids (acetylcarnitine and l-carnitine). It was concluded that supplementing the steer ration with Na2SO4 was beneficial for improving the rumen fermentation, fiber digestibility, and nutrient metabolism through modulating the rumen microbial community. IMPORTANCE Essential elements like nitrogen and sulfur greatly affect rumen fermentation and metabolism in ruminants. However, little knowledge is available on the effects of sulfur on the rumen microbiota and plasma metabolome. The results of the present trial demonstrated that supplementing the steer ration with sodium sulfate markedly improved rumen fermentation, fiber digestibility, and metabolism of amino acids, purine derivatives, and vitamins through effects on the ruminal microbiome. The facts obtained from the present trial clarified the possible mechanisms of the positive effects of sulfur on rumen fermentation and nutrient utilization.

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