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 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 PSVI-22 Fecal microbiome of dairy calves fed with different liquid diets

2020 ◽  
Vol 98 (Supplement_4) ◽  
pp. 431-431
Author(s):  
Gercino F Virgínio Júnior ◽  
Marina Coelho ◽  
Marcos Silva ◽  
Horácio Montenegro ◽  
Luiz Coutinho ◽  
...  
Keyword(s):  
Animal Health ◽  
Illumina Miseq ◽  
Diversity Indices ◽  
Liquid Diet ◽  
Intestinal Microbiome ◽  
Milk Replacer ◽  
Rrna Gene ◽  
Fecal Microbiome ◽  
Bacterial Phyla ◽  
Whole Milk

Abstract Feeding a liquid diet to the newborn calf has considerable implications for the development of the intestinal microbiota, as its composition can shift population to a highly adapted microbiota. Milk acidification may positively affect microorganisms that are beneficial to the intestine health. The present study evaluated 15 Holstein calves housed in tropical shelters, fed one of the three liquid diets: I – whole milk (n = 5), II – milk replacer (22.9 % CP; 18.5 % fat; diluted to 14% solids; n = 5) and III - whole milk acidified to pH 4.5 with formic acid (n = 5). All animals received 6 L of liquid diet, divided into two meals, being weaned at the 8th week of age. After weaning, all calves were group housed and fed with starter concentrate and coast-cross hay ad libitum. To evaluate the microbioma, 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. The diversity indices and evenness were higher for whole milk when compared to milk replacer (P < 0,05), with no difference for acidified whole milk. Animal age affected all indices. Time 0 had higher richness and diversity (P < 0,001), while weeks 1 and 2 had the lowest (P < 0,001). Thirty-eight bacterial phyla were identified, and the most abundant in were Bacteroidota, Firmicutes_A, Firmicutes, Proteobacteria and Firmicutes C. It is possible to modify the microbiome by changing the liquid diet. However, differences according to calf age may show the best time for possible interventions in the diet to manipulate the intestinal microbiome to improve animal health and performance.

scholarly journals PSIX-16 Investigating the development of the fecal microbiome in growing diary calves

2020 ◽  
Vol 98 (Supplement_4) ◽  
pp. 423-424
Author(s):  
Emily Fowler ◽  
Benoit St-Pierre
Keyword(s):  
Process Development ◽  
Bacterial Species ◽  
Pcr Amplification ◽  
Illumina Miseq ◽  
Dairy Calves ◽  
Rank Test ◽  
Rrna Gene ◽  
Microbial Succession ◽  
Fecal Microbiome ◽  
Time Points

Abstract Development of the gut microbiome in young animals is critical for maximizing productivity in adults through beneficial functional contributions of symbiotic microbial communities to the health and nutrition of their host. To gain further insight into this process, development of the fecal microbiome in 12 dairy calves was investigated. Fecal bacterial composition was determined at four time points (weeks 0, 4, 8 and 12) using the 16S rRNA gene through PCR-amplification of the V1-V3 regions from fecal microbial genomic DNA, followed by Illumina MiSeq 2X300 sequencing. A comparative analysis of the most highly represented Operational Taxonomic Units (OTU) using the non-parametric Kruskal-Wallis sum-rank test and Wilcoxon pairwise test identified both known and uncharacterized fecal bacterial species whose abundance fluctuated during development of the calves. Four highly represented OTUs were found to have a peak of abundance at week 0, which was followed by significantly lower abundance at later time points (P < 0.05). Notably, OTU JA_ 89-27339, peaked at week 0 (39.3% ± 3.6%), then declined at later time points with respective means of 2.3%, 0.1% and 0.05%. Seven other OTUs were found to peak at an intermediate time point (P < 0.05), including OTU JA_46-21334 which was found in highest abundance at week 4 (4.5% ± 1.2%) compared to means with a range of 0.001% to 0.01% for the other time points. In contrast, another set of well represented OTUs were found to increase in abundance with time, which included OTU JA_84-17601 whose abundance was highest at week 12 (1.4% ± 0.3%) (P < 0.05). These results are indicative of microbial succession in the gastrointestinal tract of dairy calves and highlight candidate bacterial species whose function could be manipulated towards improving the health and productivity of growing dairy calves.

scholarly journals Does algae β-glucan affect the fecal bacteriome in dairy calves?

PLoS ONE ◽  
2021 ◽  
Vol 16 (9) ◽  
pp. e0258069
Author(s):  
Gercino Ferreira Virginio Junior ◽  
Maria Eduarda Reis ◽  
Ana Paula da Silva ◽  
Ariany Faria de Toledo ◽  
Amanda Moelemberg Cezar ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Illumina Miseq ◽  
Dairy Calves ◽  
Milk Replacer ◽  
Rrna Gene ◽  
Health Promoting ◽  
Miseq Platform ◽  
Control Milk ◽  
And Performance ◽  
Highly Correlated

β-glucans has been reported to be associated with many health-promoting and improvements in animal performance, however, information about their effects on the bacterial community remains unknown. This study aimed to investigate how the addition of β-glucans can affect the fecal bacterial community with possible consequences on animal growth and health. For this, newborn Holstein calves (n = 14) were individually housed in tropical shelters and blocked according to sex, date, and weight at birth and randomly assigned to one of the following treatments: (1) Control: milk replacer (14% solids, 24% CP, 18.5% fat); (2) β-glucans: milk replacer supplemented with β-glucans (2 g/d). All calves were bucket fed 6 L/d of milk replacer and received water and starter concentrate ad libitum starting on d 2. To evaluate the bacteriome, fecal samples were collected at weeks 1, 2, 4, and 8. The bacterial community was assessed through sequencing of the V3-V4 region of the 16S rRNA gene on the Illumina MiSeq platform and analyzed using the DADA2 pipeline. No differences for Shannon and Chao1 indexes were observed for treatments, but both indexes increased with age (P < 0.001). There were dissimilarities in the structure of the bacterial community during the pre-weaning period (P = 0.01). In a deeper taxonomic level, Collinsella (Actinobacteriota), Prevotella (Bacteroidota), and Lactobacillus (Firmicutes) were the most abundant genera (9.84, 9.54, and 8.82% of the sequences, respectively). β-glucans promoted a higher abundance of Alloprevotella and Holdemanella, which may indicate a beneficial effect of supplementation on dairy calves. The bacterial community was highly correlated with the fecal score at weeks 1 and 2 and with starter concentrate intake at week 8. In conclusion, algae β-glucan supplementation could be beneficial to fecal bacteriome and consequently to the health and performance of dairy calves.

scholarly journals The Fecal Bacterial Microbiota in Horses with Equine Recurrent Uveitis

Animals ◽  
2021 ◽  
Vol 11 (3) ◽  
pp. 745
Author(s):  
Michelle Martin de Bustamante ◽  
Diego Gomez ◽  
Jennifer MacNicol ◽  
Ralph Hamor ◽  
Caryn Plummer
Keyword(s):  
Beta Diversity ◽  
High Throughput Sequencing ◽  
Illumina Miseq ◽  
Diversity Indices ◽  
Rrna Gene ◽  
Linear Discriminant ◽  
Alpha And Beta Diversity ◽  
Bacterial Microbiota ◽  
Healthy Control ◽  
Equine Recurrent Uveitis

The objective of this study was to describe and compare the fecal bacterial microbiota of horses with equine recurrent uveitis (ERU) and healthy horses using next-generation sequencing techniques. Fecal samples were collected from 15 client-owned horses previously diagnosed with ERU on complete ophthalmic examination. For each fecal sample obtained from a horse with ERU, a sample was collected from an environmentally matched healthy control with no evidence of ocular disease. The Illumina MiSeq sequencer was used for high-throughput sequencing of the V4 region of the 16S rRNA gene. The relative abundance of predominant taxa, and alpha and beta diversity indices were calculated and compared between groups. The phyla Firmicutes, Bacteroidetes, Verrucomicrobia, and Proteobacteria predominated in both ERU and control horses, accounting for greater than 60% of sequences. Based on linear discriminant analysis effect size (LEfSe), no taxa were found to be enriched in either group. No significant differences were observed in alpha and beta diversity indices between groups (p > 0.05 for all tests). Equine recurrent uveitis is not associated with alteration of the gastrointestinal bacterial microbiota when compared with healthy controls.

scholarly journals Faecal Microbiota of Dogs Offered a Vegetarian Diet with or without the Supplementation of Feather Meal and either Cornmeal, Rye or Fermented Rye: A Preliminary Study

2020 ◽  
Vol 8 (9) ◽  
pp. 1363
Author(s):  
Julia Hankel ◽  
Amr Abd El-Wahab ◽  
Richard Grone ◽  
Birgit Keller ◽  
Eric Galvez ◽  
...  
Keyword(s):  
Intestinal Microbiota ◽  
Hypervariable Region ◽  
Illumina Miseq ◽  
Vegetarian Diet ◽  
Rrna Gene ◽  
Feather Meal ◽  
Illumina Miseq Platform ◽  
Faecal Samples ◽  
Miseq Platform ◽  
Preliminary Study

Anthropomorphism of dogs has affected feeding and the choice of components present in diets for dogs. Conflicting trends are present: raw or vegetarian appear more prevalent. Animal-derived proteins seem to have unfavourable impacts on intestinal microflora by decreasing the presence of Bacteroidetes. This preliminary study evaluates whether effects of diets with animal proteins on intestinal microbiota can be compensated by the addition of certain carbohydrates to dog diet. Eight female beagles were included in a cross-over study and fed a vegetarian diet or the same diet supplemented with feather meal (2.7%) and either 20% of cornmeal, fermented or non-fermented rye (moisture content of the diets about 42%). A 16S rRNA gene amplification was performed within the hypervariable region V4 on faecal samples and sequenced with the Illumina MiSeq platform. The Firmicutes/Bacteroidetes ratio tended to shift to the advantage of Firmicutes when feather meal and cornmeal were added (Firmicutes/Bacteroidetes ratio of 5.12 compared to 2.47 when offered the vegetarian diet) and tended to switch back to the advantage of Bacteroidetes if rye: fermented (2.17) or not (1.03) was added. The addition of rye might have the potential to compensate possible unfavourable effects of diets with animal proteins on intestinal microbiota of dogs.

scholarly journals A Plant Growth-Promoting Microbial Soil Amendment Dynamically Alters the Strawberry Root Bacterial Microbiome

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Siwen Deng ◽  
Heidi M.-L. Wipf ◽  
Grady Pierroz ◽  
Ted K. Raab ◽  
Rajnish Khanna ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Soil Amendment ◽  
Bacterial Community Composition ◽  
Illumina Miseq ◽  
Amplicon Sequencing ◽  
Rrna Gene ◽  
Bacterial Microbiome ◽  
Plant Growth Promoting ◽  
Miseq Platform ◽  
Soil Rhizosphere

AbstractDespite growing interest in utilizing microbial-based methods for improving crop growth, much work still remains in elucidating how beneficial plant-microbe associations are established, and what role soil amendments play in shaping these interactions. Here, we describe a set of experiments that test the effect of a commercially available soil amendment, VESTA, on the soil and strawberry (Fragaria x ananassa Monterey) root bacterial microbiome. The bacterial communities of the soil, rhizosphere, and root from amendment-treated and untreated fields were profiled at four time points across the strawberry growing season using 16S rRNA gene amplicon sequencing on the Illumina MiSeq platform. In all sample types, bacterial community composition and relative abundance were significantly altered with amendment application. Importantly, time point effects on composition are more pronounced in the root and rhizosphere, suggesting an interaction between plant development and treatment effect. Surprisingly, there was slight overlap between the taxa within the amendment and those enriched in plant and soil following treatment, suggesting that VESTA may act to rewire existing networks of organisms through an, as of yet, uncharacterized mechanism. These findings demonstrate that a commercial microbial soil amendment can impact the bacterial community structure of both roots and the surrounding environment.

scholarly journals 21 Profiling sow vaginal and fecal and piglet gastrointestinal microbiome and the passage of sow microbiome to their progeny from birth to weaning

2019 ◽  
Vol 97 (Supplement_3) ◽  
pp. 21-21
Author(s):  
Huyen Tran ◽  
Brenda de Rodas ◽  
Manohar M Lahoti ◽  
Timothy J Johnson
Keyword(s):  
Alpha Diversity ◽  
Illumina Miseq ◽  
Amplicon Sequencing ◽  
Gastrointestinal Microbiome ◽  
Core Microbiome ◽  
Linear Discriminant ◽  
Fecal Microbiome ◽  
The Core ◽  
Vaginal Swabs ◽  
Sampling Points

Abstract The objectives of this study were 1) to profile the sow vaginal and fecal microbiome and the corresponding piglet gastrointestinal microbiome from birth to weaning, and 2) to identify the core microbiome shared between sows and piglets. A total of 226 samples collected from sows (vaginal swabs pre-farrow; fecal samples at farrow, d 3, 7, 10, 17 post-farrow) and their progenies (stomach, ileum, and colon digesta at birth, d 2, and 14 after birth) were used for the analyses of microbial community structure using 16S rRNA V4 amplicon sequencing with Illumina MiSeq. Our data indicated that the piglet and sow microbiome were quite distinct. Piglets had lower bacterial alpha diversity (chao1, richness, Shannon, Simpson indices; P &lt; 0.01) than sows across all timepoints. Beta diversity of piglets by sample types was significantly different (P &lt; 0.001) than sows by sample types when averaged across all timepoints or separation by timepoints. Feature selection by the Linear discriminant analysis effect size (LEfSe) indicated that the genera associated with piglets included those classified as Lactobacillus, unclassified Micrococcaceae, and Rothia when averaged across sampling points and sample types. Genera associated with sows included those classified as Treponema, YRC22, Unclassified RF39, Unclassified Christensenellaceae, Turicibacter, Unclassified RFP12, Unclassified F16, Collinsella, Coprococcus, Unclassified Coriobacteriaceae, and Unclassified Mogibacteriaceae. The genera shared between sow vaginal samples and piglets included those classified as Bacteroides, Fusobacterium, Haemophilus, Prevotella, Veillonella, and unclassified Clostridiadiaceae. The genera shared between sow fecal and piglet samples included those classified as Bacteroides, Lactobacillus, unclassified Clostridiadiaceae, unclassified Ruminococceae, and Prevotella. Overall, there are evidences that bacterial genera were passed from sows to piglets and influenced the microbial communities of piglets later in life.

scholarly journals Comparison of Gut Microbiota between Gentoo and Adélie Penguins Breeding Sympatrically on Antarctic Ardley Island as Revealed by Fecal DNA Sequencing

Diversity ◽  
2021 ◽  
Vol 13 (10) ◽  
pp. 500
Author(s):  
Yin-Xin Zeng ◽  
Hui-Rong Li ◽  
Wei Han ◽  
Wei Luo
Keyword(s):  
Gut Microbiota ◽  
Dietary Habits ◽  
Operational Taxonomic Unit ◽  
Illumina Miseq ◽  
Diversity Indices ◽  
Rrna Gene ◽  
Fildes Peninsula ◽  
Adélie Penguins ◽  
Penguin Species ◽  
Pygoscelid Penguins

There are two pygoscelid penguins, the Gentoo (Pygoscelis papua Forster, 1781) and Adélie (P. adeliae Hombron and Jacquinot, 1841) penguins, breeding sympatrically on Ardley Island, Fildes Peninsula region, South Shetlands, Antarctica. Whether the two closely related penguin species with similar dietary habits possess compositional similarity in gut microbiota remains unknown. DNA barcoding of feces is an emerging approach for gut microbiota analysis of protected animals. In the present study, the 16S rRNA gene from penguin feces was sequenced using the Illumina MiSeq platform to investigate the gut microbiota of the two pygoscelid penguin species. The fecal community of Gentoo penguins has higher diversity indices and OTU (operational taxonomic unit) richness compared to Adélie penguins. Besides unclassified bacteria, sequences fell into 22 major lineages of the domain Bacteria: Acidobacteria, Actinobacteria, Armatimonadetes, Bacteroidetes, Chlamydiae, Chloroflexi, Cloacimonetes, Cyanobacteria, Deinococcus-Thermus, Fibrobacteres, Firmicutes, Fusobacteria, Gemmatimonadetes, Ignavibacteriae, Planctomycetes, Proteobacteria, Tenericutes, Verrucomicrobia, and candidate divisions BRC1, SR1, WPS-2, and Saccharibacteria. Among these, Firmicutes (37.7%), Proteobacteria (23.1%, mainly Gamma- and Betaproteobacteria), Fusobacteria (14.3%), Bacteroidetes (7.9%), and Actinobacteria (6.6%) were dominant in the fecal microbiota of the two penguin species. At the same time, significantly higher abundances of Actinobacteria and Cyanobacteria were detected in Gentoo penguins than in Adélie penguins (p < 0.05). Overall, there was a clear difference in the composition of gut microbiota between the Adélie and Gentoo penguins. The results suggested that both the phylogeny of penguin species and the diet could be responsible for the differences in the gut microbiota of the two pygoscelid penguins breeding in the same area.

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