scholarly journals Ruminal and Fecal Bacteriome of Dairy Calves Fed Different Levels and Sources of NDF

Animals ◽  
2021 ◽  
Vol 11 (9) ◽  
pp. 2705
Author(s):  
Gercino Ferreira Virgínio Júnior ◽  
Ana Paula da Silva ◽  
Ariany Faria de Toledo ◽  
Milaine Poczynek ◽  
Amanda Moelemberg Cezar ◽  
...  
Keyword(s):  
Basal Diet ◽  
Diversity Indices ◽  
Dairy Calves ◽  
Rrna Gene ◽  
Ruminal Fluid ◽  
Fecal Samples ◽  
Α Diversity ◽  
Holstein Calves ◽  
Hind Gut ◽  
Different Levels

A starter concentrate containing different levels and sources of NDF can modify the gastrointestinal bacteriome. This study evaluated 18 Holstein calves housed in un-bedded suspended individual cages, fed one of three treatments: 22NDF: a conventional starter containing 22% NDF (n = 7); 31NDF: a starter with 31% NDF, replacing part of the corn by soybean hull (n = 6); and 22Hay: diet 22NDF plus coast-cross hay ad libitum (n = 5). All animals received 4 L of milk replacer daily, weaned at 8th week of age, and housed in wood shelters until week 10. To evaluate the bacteriome, the bacterial community of ruminal fluid and fecal samples was determined by sequencing V3 and V4 region amplicons of the 16S rRNA gene. Bacterial diversity in rumen was not affected by diet or age. The phyla Firmicutes and Bacteroidota, and Prevotella’ genus were the most abundant in ruminal fluid and fecal samples. In feces, the α-diversity indices were higher for 22Hay. All indices were significantly affected by age. We believe that the ruminal bacteriome was affected by basal diet components, but not affected by NDF levels or sources. The supply of hay was effective in modifying the fecal bacteriome of dairy calves due to hind gut fermentation.

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

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.

scholarly journals PSIX-1 Fecal microbiome of dairy calves fed with fresh or frozen maternal colostrum or colostrum powder

2020 ◽  
Vol 98 (Supplement_4) ◽  
pp. 419-419
Author(s):  
Gercino F Virgínio Júnior ◽  
Cristiane Tomaluski ◽  
Ana Paula Silva ◽  
Sophia Dondé ◽  
Horácio Montenegro ◽  
...  
Keyword(s):  
Bacterial Colonization ◽  
Illumina Miseq ◽  
Well Being ◽  
Diversity Indices ◽  
Dairy Calves ◽  
Rrna Gene ◽  
Fecal Samples ◽  
Fecal Microbiome ◽  
Bacteria Growth ◽  
Miseq Platform

Abstract Besides the importance for passive immune transfer, the supply of colostrum accelerates the bacterial colonization of the calf small intestine by providing nutrients, that will function as bacteria growth substrate, as well being a microorganism inoculum source. However, it is not known whether the effect is maintained when the calves are fed with frozen colostrum or colostrum powder. The present work evaluated 15 Holstein calves housed in tropical shelters, fed one of the colostrum sources: I – fresh colostrum from the dam (n = 5), II – frozen colostrum and III – colostrum powder, a dose of 150g of IgG (n = 5). Animals fed with fresh or frozen colostrum received a corresponding volume 10% of its birth weight of high-quality colostrum (IgG > 50g / L). All animals were fed within 4h after birth. From the second meal, calves received 6 L of liquid diet, divided into two meals, being weaned at the 8th week of age. After weaning, calves were grouped housed, and fed with starter and coast-cross hay ad libitum. To evaluate the microbiome, fecal samples were collected at birth 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. There was no treatment effect for the diversity indices, evenness and richness. Simpson’s diversity and evenness had no effect for weeks. Weeks 1 and 2 had less Shannon’ diversity. Richness was higher for week 0. Analyzing the relative abundance, 31 phyla were identified in the fecal samples, the most abundant being Bacteriodota, Firmicutes_A, Proteobacterias, Fusobacteriota and Firmicutes. Different sources of colostrum can be used to feed dairy calves, without affecting the diversity in the colonization of the intestinal tract.

scholarly journals A Combined Analysis of Gut and Skin Microbiota in Infants with Food Allergy and Atopic Dermatitis: A Pilot Study

Nutrients ◽  
2021 ◽  
Vol 13 (5) ◽  
pp. 1682
Author(s):  
Ewa Łoś-Rycharska ◽  
Marcin Gołębiewski ◽  
Marcin Sikora ◽  
Tomasz Grzybowski ◽  
Marta Gorzkiewicz ◽  
...  
Keyword(s):  
Atopic Dermatitis ◽  
Food Allergy ◽  
Gut Microbiota ◽  
Bacterial Species ◽  
Rrna Gene ◽  
Healthy Children ◽  
Skin Microbiota ◽  
Fecal Samples ◽  
Healthy Infants ◽  
Α Diversity

The gut microbiota in patients with food allergy, and the skin microbiota in atopic dermatitis patients differ from those of healthy people. We hypothesize that relationships may exist between gut and skin microbiota in patients with allergies. The aim of this study was to determine the possible relationship between gut and skin microbiota in patients with allergies, hence simultaneous analysis of the two compartments of microbiota was performed in infants with and without allergic symptoms. Fifty-nine infants with food allergy and/or atopic dermatitis and 28 healthy children were enrolled in the study. The skin and gut microbiota were evaluated using 16S rRNA gene amplicon sequencing. No significant differences in the α-diversity of dermal or fecal microbiota were observed between allergic and non-allergic infants; however, a significant relationship was found between bacterial community structure and allergy phenotypes, especially in the fecal samples. Certain clinical conditions were associated with characteristic bacterial taxa in the skin and gut microbiota. Positive correlations were found between skin and fecal samples in the abundance of Gemella among allergic infants, and Lactobacillus and Bacteroides among healthy infants. Although infants with allergies and healthy infants demonstrate microbiota with similar α-diversity, some differences in β-diversity and bacterial species abundance can be seen, which may depend on the phenotype of the allergy. For some organisms, their abundance in skin and feces samples may be correlated, and these correlations might serve as indicators of the host’s allergic state.

199 Do the Microbiomes of Horses Process Nutrients Differently Based on Keeper Status?

2021 ◽  
Vol 99 (Supplement_3) ◽  
pp. 106-106
Author(s):  
Alexa C Johnson ◽  
Amy S Biddle
Keyword(s):  
Fixed Effects ◽  
High Performance ◽  
16S Rrna Gene Sequencing ◽  
Gas Production ◽  
Rrna Gene ◽  
Total N ◽  
Fermentation Products ◽  
Fecal Samples ◽  
Α Diversity ◽  
C 50

Abstract This study reports the differential response of the equine gut microbiome to protein and/or carbohydrate based on keeper status (easy keeper (EK), medium keeper (MK), hard keeper (HK)). Anaerobic equine fecal samples (n = 12 total, n = 3 / EK, MK, HK of four breeds) inoculated microcosms with three dietary conditions (C = Carb (cornmeal), P = Protein (soybean meal), and M = mix (50% C, 50% P)). Over 48 hours, fermentation products were measured using colorimetric assays and high-performance liquid chromatography. Microbial populations were surveyed using 16S rRNA gene sequencing analyzed by QIIME2. Linear mixed models were fit with fixed effects of Treatment and Keeper status and their interactions, with random effects of HorseID. Differences in fermentation products by keeper status included: MK had higher pH and greater gas production, EK produced higher hydrogen sulfide, and HK had greater total protein. Total SCFA was not different between keeper status (P = 0.89) but the acetate: propionate ratio was highest for HK (2.45mM) and lowest for EK (1.85mM) (P = 0.05). Isobutyrate production was highest in HK (2.34mM) compared to MK (0.85mM) and EK (0.17mM). Treatment had significant effects across all measurements; M and C treatment values were similar reflecting microbial preferences for carbohydrates before protein. P treated trials had increased fermentation outputs due to lower acidity effects. Keeper status had no effect on α-diversity (P > 0.05) however HK horses were least affected by treatments. P treated samples were more diverse than C and M (P < 0.001). Spearman correlation of Keeper x Treatment identified Oligosphaeria spp. in EK (r = 0.49) and Fusobacteria spp. in HK whole fecal samples (r = 0.37). These data suggest that while the compositions of the gut microbiomes of keeper groups were similar, they were functionally different in processing key nutrients.

scholarly journals Garlic skin induced shifts in the rumen microbiome and metabolome of fattening sheep

2020 ◽  
Author(s):  
Wen Zhu ◽  
Zhen Su ◽  
Wei Xu ◽  
Hanxue Sun ◽  
Jinfeng Gao ◽  
...  
Keyword(s):  
Growth Performance ◽  
Average Daily Gain ◽  
Basal Diet ◽  
Diversity Indices ◽  
Rumen Fermentation ◽  
Control Group ◽  
Rumen Microbiome ◽  
Volatile Fatty Acid Concentration ◽  
Α Diversity ◽  
Daily Gain

Abstract Background Garlic and its constituents exhibit activities on modifying rumen fermentation and improving growth performance. As a by-product of garlic processing, garlic skin contains similar bioactive components as garlic bulb. However, studies in ruminants using garlic skin are scarce. This study was conducted to investigate the effects of garlic skin supplementation on rumen fermentation characterizes, growth performance, ruminal microbes and metabolites in ruminants. Twelve Hu lambs were randomly assigned into one of two treatments: basal diet (CON) or basal diet supplemented with 80 g/kg DM of gallic skin (GAS). The experiment lasted for10 weeks, with the first 2 weeks for adaptation. Results The results revealed that the average daily gain and volatile fatty acid concentration were higher (P < 0.05) in lambs fed GAS than that in the control group. Garlic skin supplementation did not significantly (P > 0.10) affect the α-diversity indices. Increased (P < 0.05) abundances of Prevotella, Bulleidia, Howardella, Methanosphaera but a decreased (P < 0.05) abundance of Fretibacterium were observed in GAS-fed lambs. In addition, the garlic skin supplementation favorably regulated (P < 0.05) pyrimidine metabolism, purine metabolism, vitamin B6 and B1 metabolism. Moreover, high correlations were observed between fluctuant rumen microbiota and metabolites. Conclusions Supplementation of garlic skin improved the growth performance of sheep by modifying rumen fermentation through inducing shifts in the rumen microbiome and metabolome.

scholarly journals Fecal microbiome profiles of neonatal dairy calves with varying severities of gastrointestinal disease

PLoS ONE ◽  
2022 ◽  
Vol 17 (1) ◽  
pp. e0262317
Author(s):  
Giovana S. Slanzon ◽  
Benjamin J. Ridenhour ◽  
Dale A. Moore ◽  
William M. Sischo ◽  
Lindsay M. Parrish ◽  
...  
Keyword(s):  
Health Status ◽  
Relative Abundance ◽  
Gastrointestinal Disease ◽  
Bifidobacterium Longum ◽  
Dairy Calves ◽  
Rrna Gene ◽  
Probiotic Properties ◽  
Fecal Samples ◽  
Fecal Microbiome ◽  
Microbiome Composition

Gastrointestinal disease (GI) is the most common illness in pre-weaned dairy calves. Studies have associated the fecal microbiome composition with health status, but it remains unclear how the microbiome changes across different levels of GI disease and breeds. Our objective was to associate the clinical symptoms of GI disease with the fecal microbiome. Fecal samples were collected from calves (n = 167) of different breeds (Holstein, Jersey, Jersey-cross and beef-cross) from 4–21 d of age. Daily clinical evaluations assessed health status. Calves with loose or watery feces were diagnosed with diarrhea and classified as bright-sick (BS) or depressed-sick (DS) according to behavior. Calves with normal or semiformed feces and no clinical illness were classified as healthy (H). One hundred and three fecal samples were obtained from consistently healthy calves and 64 samples were from calves with diarrhea (n = 39 BS; n = 25 DS). The V3-V4 region of 16S rRNA gene was sequenced and analyzed. Differences were identified by a linear-mixed effects model with a negative binomial error. DS and Jersey calves had a higher relative abundance of Streptococcus gallolyticus relative to H Holstein calves. In addition, DS calves had a lower relative abundance of Bifidobacterium longum and an enrichment of Escherichia coli. Species of the genus Lactobacillus, such as an unclassified Lactobacillus, Lactobacillus reuteri, and Lactobacillus salivarius were enriched in calves with GI disease. Moreover, we created a model to predict GI disease based on the fecal microbiome composition. The presence of Eggerthella lenta, Bifidobacterium longum, and Collinsella aerofaciens were associated with a healthy clinical outcome. Although lactobacilli are often associated with beneficial probiotic properties, the presence of E. coli and Lactobacillus species had the highest coefficients positively associated with GI disease prediction. Our results indicate that there are differences in the fecal microbiome of calves associated with GI disease severity and breed specificities.

scholarly journals Economic evaluation and efficacy of strategic-selective treatment of gastrointestinal parasites in dairy calves

2017 ◽  
Vol 26 (2) ◽  
pp. 123-128 ◽  
Author(s):  
Yuly Andrea Caicedo Blanco ◽  
Jonata de Melo Barbieri ◽  
Renato Ribeiro de Lima ◽  
Marcos Aurélio Lopes ◽  
Eduardo Mitke Brandão Reis ◽  
...  
Keyword(s):  
Economic Evaluation ◽  
Statistical Analysis ◽  
Conventional Treatment ◽  
Average Frequency ◽  
Gastrointestinal Parasites ◽  
Dairy Calves ◽  
Operational Cost ◽  
Selective Treatment ◽  
Fecal Samples ◽  
Holstein Calves

Abstract In the Experimental Farm of the Universidade Federal de Lavras (EF-UFLA), state of Minas Gerais, Brazil, on their day of birth, female Holstein calves were randomly selected and placed into two groups containing fifteen animals each: Strategic-Selective Treatment (S-ST) or Conventional Treatment (CT). In the S-ST, calves were treated after coproparasitological examinations according to criteria established previously by the researchers. Calves in the CT were treated according to the opinion of the veterinarian of EF-UFLA. For statistical analysis, the frequency (%) of fecal samples with count of eggs per gram of feces (EPG) ≥300, count of oocysts per gram of feces (OoPG) ≥500 and fecal samples with count of cysts of Giardia spp. ≥1 were conducted. The overall average frequency of fecal samples with EPG ≥300, OoPG ≥500 and Giardia spp. cysts ≥1, respectively, was similar (p >0.05) between S-ST (20.3%; 17.3%; and 31.5%) and CT (26.4%; 23.9%; and 37.3%). The effective operational cost, per animal, in 12 months, was of R$ 784.58 (US$ 241.41) and R$ 83.90 (US$ 25.81) in S-ST and CT, respectively. The S-ST requires adjustments to be used as a technically efficient and economically viable alternative for the control of gastrointestinal parasitosis in female Holstein calves.

Seasonal dynamics of the bacterioplankton community in a large, shallow, highly dynamic freshwater lake

2018 ◽  
Vol 64 (11) ◽  
pp. 786-797 ◽  
Author(s):  
Zhaoyu Kong ◽  
Wenbo Kou ◽  
Yantian Ma ◽  
Haotian Yu ◽  
Gang Ge ◽  
...  
Keyword(s):  
Water Level ◽  
Relative Abundance ◽  
Poyang Lake ◽  
Nutrient Status ◽  
Diversity Indices ◽  
Freshwater Lake ◽  
Rrna Gene ◽  
Bacterioplankton Community ◽  
Α Diversity ◽  
Composition Structure

The spatiotemporal shifts of the bacterioplankton community can mirror their transition of functional traits in an aquatic ecosystem. However, the spatiotemporal variation of the bacterioplankton community composition structure (BCCS) within a large, shallow, highly dynamic freshwater lake is still poorly understood. Here, we examined the seasonal and spatial variability of the BCCs within Poyang Lake by sequencing the 16S rRNA gene amplicon to explore how hydrological changes affect the BCCs. Principal coordinate analysis showed that the BCCs varied significantly among four sampling seasons, but not spatially. The seasonal changes of the BCCs were mainly attributed to the differences between autumn and spring–winter. Higher α diversity indices were observed in autumn. Redundancy analysis indicated that the BCCs co-variated with water level, pH, temperature, total phosphorus, ammoniacal nitrogen, electrical conductivity, total nitrogen, and turbidity. Among them, water level was the key determinant separating autumn BCCs from the BCCs in other seasons. A significantly lower relative abundance of Burkholderiales (betI and betVII) and a higher relative abundance of Actinomycetales (acI, acTH1, and acTH2) were found in autumn than in other seasons. Overall, our results suggest that water level changes associated with pH, temperature, and nutrient status shaped the seasonal patterns of the BCCs within Poyang Lake.

scholarly journals Garlic Skin Induced Shifts in the Rumen Microbiome and Metabolome of Fattening Sheep

2020 ◽  
Author(s):  
WEN Zhu ◽  
Zhen Su ◽  
Wei Xu ◽  
Hanxue Sun ◽  
Jinfeng Gao ◽  
...  
Keyword(s):  
Growth Performance ◽  
Average Daily Gain ◽  
Basal Diet ◽  
Diversity Indices ◽  
Rumen Fermentation ◽  
Control Group ◽  
Rumen Microbiome ◽  
Volatile Fatty Acid Concentration ◽  
Α Diversity ◽  
Daily Gain

Abstract Background: Garlic and its constituents exhibit activities on modifying rumen fermentation and improving growth performance. As a by-product of garlic processing, garlic skin contains similar bioactive components as garlic bulb. However, studies in ruminants using garlic skin are scarce. This experiment was conducted to investigate the effects of garlic skin supplementation on rumen fermentation characterizes, growth performance, and involved mechanism in ruminants. Twelve Hu lambs were randomly assigned into one of two treatments: basal diet (CON) or basal diet supplemented with 80 g/kg DM of gallic skin (GAS). The experiment lasted for10 weeks, with the first 2 weeks for adaptation. Results: The results revealed that the average daily gain and volatile fatty acid concentration were higher (P < 0.05) in lambs fed GAS than that in the control group. Garlic skin supplementation did not significantly (P > 0.10) affect the α-diversity indices. Increased (P < 0.05) abundances of Prevotella, Bulleidia, Howardella, Methanosphaera but a decreased (P < 0.05) abundance of Fretibacterium were observed in GAS-fed lambs. Besides, the garlic skin supplementation favorably regulated (P < 0.05) pyrimidine metabolism, purine metabolism, vitamin B6 and B1 metabolism. Moreover, high correlations were observed between fluctuant rumen microbiota and metabolites. Conclusions: Supplementation of garlic skin improved the growth performance of sheep by modifying rumen fermentation through inducing shifts in the rumen microbiome and metabolome.

scholarly journals Identification of Enterotype and Its Effects on Intestinal Butyrate Production in Pigs

Animals ◽  
2021 ◽  
Vol 11 (3) ◽  
pp. 730
Author(s):  
E Xu ◽  
Hua Yang ◽  
Minmin Ren ◽  
Yuanxia Wang ◽  
Mingfei Xiao ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Bacterial Community Composition ◽  
Short Chain Fatty Acids ◽  
Diversity Indices ◽  
Sensu Stricto ◽  
Shannon Index ◽  
Nutrient Metabolism ◽  
Fecal Samples ◽  
Coa Transferase ◽  
Α Diversity

Gut microbiota is thought to play a crucial role in nutrient digestion for pigs, especially in processing indigestible polysaccharides in the diets to produce short-chain fatty acids (SCFAs). However, the link between microbiota community structure and phenotypic performances are poorly understood. In the present study, the fecal samples of 105 Jinhua pigs at 105 days of age were clustered into three enterotypes (ETs, ET1, ET2, and ET3) that are subpopulations of distinct bacterial community composition by using 16S rRNA high throughput sequencing. The α-diversity indices (the OTU number and Shannon index) were significantly different among the ETs (p < 0.001). At the genus level, the ET1 group was over-represented by Lactobacillus (17.49%) and Clostridium sensu stricto 1 (11.78%), the ET2 group was over-represented by Clostridium sensu stricto 1 (17.49%) and Bifidobacterium (11.78%), and the ET3 group was over-represented by Bacteroides (18.17%). Significant differences in the fecal contents of butyrate were observed among ETs, with the highest level detected in ET3 and the lowest in ET2 (p < 0.05). Consistently, more copies of the terminal genes for butyrate synthesis, butyrate kinase (Buk) and butyryl coenzyme A (CoA): acetate CoA transferase (But) were detected by qPCR in the fecal samples of the ET3 group as compared to other two groups (p < 0.05). In addition, of the two genes, But was demonstrated to be more relevant to the butyrate content (R = 0.7464) than Buk (R = 0.4905) by correlation analysis. In addition, based on the taxonomic analysis, we found that Faecalibacterium was the most relevant butyrate-producing genera with fecal butyrate contents in Jinhua pigs, followed by Butyricicoccus, Eubacterium, Butyricimonas, Blautia, and Anaerostipes, all of which showed significantly higher richness in ET3 than as compared to ET1 and ET2 (p < 0.05). Collectively, this work presents a first overview of the enterotypes clustering in Jinhua pigs and will help to unravel the functional implications of ETs for the pig’s phenotypic performance and nutrient metabolism.

Sign in / Sign up

Export Citation Format

Share Document