Effects of steam-flaked grains on foals’ growth and faecal microbiota

Abstract Background There is little objective information concerning the effect of steam-flaked grains on foal’s growth performance and faecal microbiota. To determine the effects of steam-flaked grains on foal’s growth performance and faecal microbiota, faecal samples were collection from 18 foals which had been fed either corn, oat or barley diets over the 60 days of the experiment. Body weight and conformation measurements were collected. Next-generation sequencing of the V3 + V4 region of the 16 S rRNA gene was used to assess the microbial composition of faeces. Alpha diversity, Venn graph, Relative abundance and beta diversity are presented. Results There was a significantly higher larger increase in the body weight of those foals fed barley compared to either corn or oats. There were also significant changes in the Alpha diversity of the gut microbiota. The Shannon and Simpson indices were significantly higher in the barley fed group than those fed corn or oats. The Chao1 index was significantly higher in the oat fed group than the corn or barley fed groups. There were significant changes in the relative abundance of bacteria in the microbiota in terms of phylum, family and genus. The histogram of LDA value distribution showed that the 12 statistically different biomarkers of the bacteria were present. Tax4Fun function annotation clustering heat map showed that functional information was detected from 26 species of bacteria in faecal samples from the foals. Conclusions Differences by starch sources were found in overall growth of the foals and in the faecal microbiota if either supplementary corn, oat or barley was fed. Further studies are required to determine the potential impact of the changes in the microbiota on the health and development of foals fed cereal starch of different sources.

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Effects of Steam-Flaked Grains On Foals Growth Performance And Faecal Microbiota

10.21203/rs.3.rs-506060/v1 ◽

2021 ◽

Author(s):

XiaoBin Li ◽

Xin Xin Huang ◽

Chang Jiang Zang ◽

Chen Ma ◽

Kai Xu Chen ◽

...

Keyword(s):

Body Weight ◽

Weight Gain ◽

Growth Performance ◽

Relative Abundance ◽

Alpha Diversity ◽

The Body ◽

Daily Weight Gain ◽

Rrna Gene ◽

Faecal Microbiota ◽

Microbial Composition

Abstract BackgroundThere is little objective information concerning the effect of steam-flaked grains on foal’s growth performance and faecal microbiota.To determine the effects of steam-flaked grains on foal’s growth performance and faecal microbiota.Faecal samples were collection from 18 foals which had been fed corn, oat or barley diets over the 60 days of the experiment. Body weight and measurements were collected. Next-generation sequencing of the V3+V4 region of the 16S rRNA gene was used to assess the microbial composition of faeces. Alpha diversity, Venn graph, Relative abundance and beta diversity are presented.ResultsThere was a significantly higher increase in the body weight of those foals fed barley compared to either corn or oats, both in terms of the total weight gain and the daily weight gain (P=0.0185). There were also significant changes in the Alpha diversity. The Shannon and Simpson indices were higher in the barley fed group than those fed corn or oats (P<0.05, P<0.05, P<0.05 and P<0.05). The Chao1 index was higher in the oat fed group than the corn or barley fed groups (P<0.05 and P<0.05). There were significant changes in the relative abundance of bacteria in the microbiota in terms of phylum, family and genus. The histogram of LDA value distribution showed that the statistically different biomarkers of the bacteria was 12. Tax4Fun function annotation clustering heat map showed that functional information was detected from 26 species of bacteria in faecal samples from the foals.ConclusionsDifferences were seen in the faecal microbiota of foals fed either corn, oat or barley, and also differences in the overall growth of the foals. Different grains have different impact on faecal microbiota, which are mainly related to the grain sources. Further investigation is required to look at the potential impact of changes in the microbiota on the functional impact on foals when fed grains.

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Comparison of targeted metagenomics and IS-Pro methods for analysing the lung microbiome

BMC Microbiology ◽

10.1186/s12866-021-02288-x ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

T Goolam Mahomed ◽

RPH Peters ◽

GHJ Pretorius ◽

A Goolam Mahomed ◽

V Ueckermann ◽

...

Keyword(s):

Relative Abundance ◽

Alpha Diversity ◽

Species Level ◽

Rrna Gene ◽

Microbial Composition ◽

Laboratory Cost ◽

Diversity Measure ◽

Lung Microbiome ◽

Copd Patients ◽

The Many

Abstract Background Targeted metagenomics and IS-Pro method are two of the many methods that have been used to study the microbiome. The two methods target different regions of the 16 S rRNA gene. The aim of this study was to compare targeted metagenomics and IS-Pro methods for the ability to discern the microbial composition of the lung microbiome of COPD patients. Methods Spontaneously expectorated sputum specimens were collected from COPD patients. Bacterial DNA was extracted and used for targeted metagenomics and IS-Pro method. The analysis was performed using QIIME2 (targeted metagenomics) and IS-Pro software (IS-Pro method). Additionally, a laboratory cost per isolate and time analysis was performed for each method. Results Statistically significant differences were observed in alpha diversity when targeted metagenomics and IS-Pro methods’ data were compared using the Shannon diversity measure (p-value = 0.0006) but not with the Simpson diversity measure (p-value = 0.84). Distinct clusters with no overlap between the two technologies were observed for beta diversity. Targeted metagenomics had a lower relative abundance of phyla, such as the Proteobacteria, and higher relative abundance of phyla, such as Firmicutes when compared to the IS-Pro method. Haemophilus, Prevotella and Streptococcus were most prevalent genera across both methods. Targeted metagenomics classified 23 % (144/631) of OTUs to a species level, whereas IS-Pro method classified 86 % (55/64) of OTUs to a species level. However, unclassified OTUs accounted for a higher relative abundance when using the IS-Pro method (35 %) compared to targeted metagenomics (5 %). The two methods performed comparably in terms of cost and time; however, the IS-Pro method was more user-friendly. Conclusions It is essential to understand the value of different methods for characterisation of the microbiome. Targeted metagenomics and IS-Pro methods showed differences in ability in identifying and characterising OTUs, diversity and microbial composition of the lung microbiome. The IS-Pro method might miss relevant species and could inflate the abundance of Proteobacteria. However, the IS-Pro kit identified most of the important lung pathogens, such as Burkholderia and Pseudomonas and may work in a more diagnostics-orientated setting. Both methods were comparable in terms of cost and time; however, the IS-Pro method was easier to use.

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The Equine Faecal Microbiota Undergoes Step-wise Compositional Changes in Accordance With Increasing Levels of Domestication

10.21203/rs.3.rs-164863/v1 ◽

2021 ◽

Author(s):

Katie Bull ◽

Gareth Davies ◽

Timothy Patrick Jenkins ◽

Laura Elizabeth Peachey

Keyword(s):

Adult Female ◽

High Throughput Sequencing ◽

Rrna Gene ◽

Faecal Microbiota ◽

Microbial Composition ◽

Faecal Samples ◽

High Incidence ◽

Life Threatening ◽

Group Variation ◽

The Uk

Abstract BackgroundChanges to the gut microbiota are associated with an increased incidence of disease in many species. This is particularly important during the process of domestication, where captive animals commonly suffer from gastrointestinal (GI) pathology. Horses are a prime example of a species which suffers from a high incidence of (often life-threatening) GI diseases in domesticated environments. We aimed to indentify the gut microbial changes which occur due to domestication in horses by profiling the faecal microbiota of adult female Exmoor ponies under three management conditions, representing increasing levels of domestication.MethodsFaecal samples were collected from 29 adult female Exmoor ponies in the South West of the UK; ponies were categorised as Feral (n=10), Semi-Feral (n=10) and Domesticated (n=9), based on their management conditions; thus controlling for age, gender and random effects between groups. Diet and medication were recorded and faecal samples taken to assess parasite infection. Faecal microbial composition was profiled via high-throughput sequencing of the bacterial 16S rRNA gene.ResultsDownstream biostatistical analysis indicated profound step-wise changes in global microbial community structure in the transition from Feral to Semi-Feral to Domesticated groups. A relatively high abundance of members of the phylum Proteobacteria and Tenericutes were associated with the Domesticated group; and higher levels of Methanobacteria were seen in the Feral group. The Semi-Feral group frequently had intermediate levels of these taxa; however, they also exhibited the greatest ‘within group’ variation in bacterial diversity and parasites burdens. Functional predictions revealed increased amino acid and lipid metabolism in the Domesticated group and increased energy metabolism in the Feral group; supporting a hypothesis that differences in diet was the key driver of gut microbial composition. ConclusionsIf assumed the Feral population has a more natural gut microbial phenotype, akin to that with which horses have evolved, these data can potentially be used to provide microbial signitures of balanced gut homeostasis in horses; which, in turn, will aid prevention of GI disease in domesticated horses.

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Effect of Dietary Yeast Culture Supplementation on the Growth Performance and Cecal Microbiota Modulation of Geese

10.21203/rs.3.rs-101816/v1 ◽

2020 ◽

Author(s):

Yating Cheng ◽

Kun Wan ◽

Zibiao Xiong ◽

Hui Luo ◽

Anfang Liu ◽

...

Keyword(s):

Body Weight ◽

Growth Performance ◽

Relative Abundance ◽

Basal Diet ◽

Feed Additives ◽

The Body ◽

Energy Utilization ◽

Yeast Culture ◽

Beneficial Bacteria ◽

Α Diversity

Abstract BackgroundOne of the most extensively applied animal feed additives is yeast culture (YC), which can increase production efficiency by altering gastrointestinal tract (GIT) microbiota. However, its use is still limited in waterfowl. Geese are the ideal model to study the interaction between dietary and GIT, due to their adaptation to consume different roughage sources. Therefore, the effect of YC supplementation at different concentrations (0%, 0.5%,1.0%,2.0% and 4.0%) on the GIT microbiota of geese was investigated in the present study. ResultsThree hundred Sichuan white geese with healthy and similar body weight (BW: 95.57 ± 2.42 g) were randomly divided into five groups: i) basal diet (control), ii) basal diet+0.5%YC (treat1), iii) basal diet+1.0% YC (treat2), iv) basal diet+2.0% YC (treat3), and v) basal diet+4.0% YC (treat4). After 10 weeks, slaughter and collected the cecum contents, then analysis GIT microbiota by high-throughput sequencing. The results showed that YC supplementation did not significantly affect α-diversity (P ＞0.05). Principal coordinates analysis showed an obvious separation between control and treat4. The dominant phyla were Firmicutes and Bacteroidetes whereas the predominant genera were Alistipes and Desulfovibrionaceae. The relative abundance of Firmicutes significantly increased in the treat1 group, whereas that of Bacteroidetes significantly decreased in the treat4 group. Dietary YC increased the proportion of beneficial bacteria, such as Parabacteroides, Enterococcus, Streptococcus and Pseudomonas, particularly in group treat2. Furthermore, treat3 significantly improved the body weight and feed utilization of geese.ConclusionCollectively, these findings demonstrate that dietary YC supplementation tends to increase species diversity and richness of GIT microbiota in geese. This increases the proportion of beneficial bacteria which improves amino acid and carbohydrate metabolism. Moreover, YC increases the relative abundance of Firmicutes that promote energy utilization and nutrition absorption, thereby improving the growth performance of geese. This dietary strategy based on feed additives is an effective method to maintain the health of the geese GIT and to improve growth efficiency.

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Host reproductive cycle influences the pouch microbiota of wild southern hairy-nosed wombats (Lasiorhinus latifrons)

Animal Microbiome ◽

10.1186/s42523-021-00074-8 ◽

2021 ◽

Vol 3 (1) ◽

Author(s):

Sesilje Weiss ◽

David Taggart ◽

Ian Smith ◽

Kristofer M. Helgen ◽

Raphael Eisenhofer

Keyword(s):

Microbial Community ◽

Reproductive Cycle ◽

Tammar Wallaby ◽

The Body ◽

Rrna Gene ◽

Microbial Composition ◽

Birth Canal ◽

Gram Positive Bacteria ◽

Rigorous Framework ◽

The 16S Rrna Gene

Abstract Background Marsupials are born much earlier than placental mammals, with most crawling from the birth canal to the protective marsupium (pouch) to further their development. However, little is known about the microbiology of the pouch and how it changes throughout a marsupial’s reproductive cycle. Here, using stringent controls, we characterized the microbial composition of multiple body sites from 26 wild Southern Hairy-nosed Wombats (SHNWs), including pouch samples from animals at different reproductive stages. Results Using qPCR of the 16S rRNA gene we detected a microbial community in the SHNW pouch. We observed significant differences in microbial composition and diversity between the body sites tested, as well as between pouch samples from different reproductive stages. The pouches of reproductively active females had drastically lower microbial diversity (mean ASV richness 19 ± 8) compared to reproductively inactive females (mean ASV richness 941 ± 393) and were dominated by gram positive bacteria from the Actinobacteriota phylum (81.7–90.6%), with the dominant families classified as Brevibacteriaceae, Corynebacteriaceae, Microbacteriaceae, and Dietziaceae. Three of the five most abundant sequences identified in reproductively active pouches had closest matches to microbes previously isolated from tammar wallaby pouches. Conclusions This study represents the first contamination-controlled investigation into the marsupial pouch microbiota, and sets a rigorous framework for future pouch microbiota studies. Our results indicate that SHNW pouches contain communities of microorganisms that are substantially altered by the host reproductive cycle. We recommend further investigation into the roles that pouch microorganisms may play in marsupial reproductive health and joey survival.

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Conventional myelosuppressive chemotherapy for non-haematological malignancy disrupts the intestinal microbiome

BMC Cancer ◽

10.1186/s12885-021-08296-4 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Lito E. Papanicolas ◽

Sarah K. Sims ◽

Steven L. Taylor ◽

Sophie J. Miller ◽

Christos S. Karapetis ◽

...

Keyword(s):

Gut Microbiota ◽

Relative Abundance ◽

Haematological Malignancy ◽

Amplicon Sequencing ◽

Intestinal Microbiome ◽

Rrna Gene ◽

Conventional Chemotherapy ◽

Myelosuppressive Chemotherapy ◽

Gram Positive Bacteria ◽

Faecal Samples

Abstract Background The gut microbiota influences many aspects of host physiology, including immune regulation, and is predictive of outcomes in cancer patients. However, whether conventional myelosuppressive chemotherapy affects the gut microbiota in humans with non-haematological malignancy, independent of antibiotic exposure, is unknown. Methods Faecal samples from 19 participants with non-haematological malignancy, who were receiving conventional chemotherapy regimens but not antibiotics, were examined prior to chemotherapy, 7–12 days after chemotherapy, and at the end of the first cycle of treatment. Gut microbiota diversity and composition was determined by 16S rRNA gene amplicon sequencing. Results Compared to pre-chemotherapy samples, samples collected 7–12 days following chemotherapy exhibited increased richness (mean 120 observed species ± SD 38 vs 134 ± 40; p = 0.007) and diversity (Shannon diversity: mean 6.4 ± 0.43 vs 6.6 ± 0.41; p = 0.02). Composition was significantly altered, with a significant decrease in the relative abundance of gram-positive bacteria in the phylum Firmicutes (pre-chemotherapy median relative abundance [IQR] 0.78 [0.11] vs 0.75 [0.11]; p = 0.003), and an increase in the relative abundance of gram-negative bacteria (Bacteroidetes: median [IQR] 0.16 [0.13] vs 0.21 [0.13]; p = 0.01 and Proteobacteria: 0.015 [0.018] vs 0.03 [0.03]; p = 0.02). Differences in microbiota characteristics from baseline were no longer significant at the end of the chemotherapy cycle. Conclusions Conventional chemotherapy results in significant changes in gut microbiota characteristics during the period of predicted myelosuppression post-chemotherapy. Further study is indicated to link microbiome changes during chemotherapy to clinical outcomes.

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PSV-19 Effect of Low Nutrient Density Diet with Probiotic Mixture (B. Subtilis ms1, B. Licheniformis SF5-1, and S. Cerevisiae) Supplementation on Performance of Weaner Pigs

Journal of Animal Science ◽

10.1093/jas/skab054.318 ◽

2021 ◽

Vol 99 (Supplement_1) ◽

pp. 193-195

Author(s):

Vetriselvi Sampath ◽

Hyun Ju Park ◽

Yong min Kim ◽

Je Min Ahn ◽

Inho Kim

Keyword(s):

Body Weight ◽

Growth Performance ◽

Average Daily Gain ◽

Nutrient Digestibility ◽

The Body ◽

Interactive Effects ◽

Low Density ◽

Gas Emission ◽

Nutrient Density ◽

Weaner Pigs

Abstract BACKGROUND: A total of one hundred and forty, 28 d-old weaner pigs [Duroc x (Yorkshire x Landrace)] with initial body weight (BW) of 6.56±1.25kg were used in a six-week treatment (7 replicate pens per treatment; barrows, and 2 gilts/pen) to evaluate the effect of low nutrient density diet supplement with probiotic mixture supplementation on the growth performance, nutrient digestibility, fecal microbial, and gas emission of weaner pigs. RESULTS: Pigs fed low-density diet with probiotic mixture supplementation had linearly increased (P = 0.028, 0.014) the body weight (BW) at weeks 3, and 6. Moreover, average daily gain (ADG) was linearly improved (P=0.018, 0.014, 0.014) at week 3, 6, and overall experiment. However, there were no interactive effects found on the nutrient digestibility of dry matter (DM), nitrogen (N) and energy (E) throughout the experiment. Dietary inclusion of low-density diet with probiotic mixture supplementation has improved the fecal lactobacillus counts linearly, but E. coli was unaffected during the trail. On day 42, Ammonium gas emission was significantly decrease in pigs fed a low-density diet with probiotic mixture supplementation. However, H2S, acetic acid, and CO2 were not significantly affected by the probiotic mixture supplementation diet. CONCLUSION: Low-density diet with probiotic mixture supplementation had positively affected the growth performance, fecal microbial, and fecal gas emission on weaner pigs.

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Experimental infection with the hookworm, Necator americanus, is associated with stable gut microbial diversity in human volunteers with relapsing multiple sclerosis

BMC Biology ◽

10.1186/s12915-021-01003-6 ◽

2021 ◽

Vol 19 (1) ◽

Author(s):

Timothy P. Jenkins ◽

David I. Pritchard ◽

Radu Tanasescu ◽

Gary Telford ◽

Marina Papaiakovou ◽

...

Keyword(s):

Multiple Sclerosis ◽

Experimental Infection ◽

High Throughput Sequencing ◽

Alpha Diversity ◽

Placebo Treatment ◽

Sequencing Data ◽

Faecal Microbiota ◽

Microbial Composition ◽

Necator Americanus ◽

Human Volunteers

Abstract Background Helminth-associated changes in gut microbiota composition have been hypothesised to contribute to the immune-suppressive properties of parasitic worms. Multiple sclerosis is an immune-mediated autoimmune disease of the central nervous system whose pathophysiology has been linked to imbalances in gut microbial communities. Results In the present study, we investigated, for the first time, qualitative and quantitative changes in the faecal bacterial composition of human volunteers with remitting multiple sclerosis (RMS) prior to and following experimental infection with the human hookworm, Necator americanus (N+), and following anthelmintic treatment, and compared the findings with data obtained from a cohort of RMS patients subjected to placebo treatment (PBO). Bacterial 16S rRNA high-throughput sequencing data revealed significantly decreased alpha diversity in the faecal microbiota of PBO compared to N+ subjects over the course of the trial; additionally, we observed significant differences in the abundances of several bacterial taxa with putative immune-modulatory functions between study cohorts. Parabacteroides were significantly expanded in the faecal microbiota of N+ individuals for which no clinical and/or radiological relapses were recorded at the end of the trial. Conclusions Overall, our data lend support to the hypothesis of a contributory role of parasite-associated alterations in gut microbial composition to the immune-modulatory properties of hookworm parasites.

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The Effects of Genetic Relatedness on the Preterm Infant Gut Microbiota

Microorganisms ◽

10.3390/microorganisms9020278 ◽

2021 ◽

Vol 9 (2) ◽

pp. 278

Author(s):

Shen Jean Lim ◽

Miriam Aguilar-Lopez ◽

Christine Wetzel ◽

Samia V. O. Dutra ◽

Vanessa Bray ◽

...

Keyword(s):

Gut Microbiota ◽

Preterm Infant ◽

Neonatal Intensive Care ◽

Genetic Relatedness ◽

Bovine Milk ◽

Alpha Diversity ◽

Neonatal Intensive Care Units ◽

Rrna Gene ◽

Microbial Composition ◽

Operational Taxonomic Units

The preterm infant gut microbiota is influenced by environmental, endogenous, maternal, and genetic factors. Although siblings share similar gut microbial composition, it is not known how genetic relatedness affects alpha diversity and specific taxa abundances in preterm infants. We analyzed the 16S rRNA gene content of stool samples, ≤ and >3 weeks postnatal age, and clinical data from preterm multiplets and singletons at two Neonatal Intensive Care Units (NICUs), Tampa General Hospital (TGH; FL, USA) and Carle Hospital (IL, USA). Weeks on bovine milk-based fortifier (BMF) and weight gain velocity were significant predictors of alpha diversity. Alpha diversity between siblings were significantly correlated, particularly at ≤3 weeks postnatal age and in the TGH NICU, after controlling for clinical factors. Siblings shared higher gut microbial composition similarity compared to unrelated individuals. After residualizing against clinical covariates, 30 common operational taxonomic units were correlated between siblings across time points. These belonged to the bacterial classes Actinobacteria, Bacilli, Bacteroidia, Clostridia, Erysipelotrichia, and Negativicutes. Besides the influence of BMF and weight variables on the gut microbial diversity, our study identified gut microbial similarities between siblings that suggest genetic or shared maternal and environmental effects on the preterm infant gut microbiota.

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Growth performance, correlation and regression estimates of seven-chicken strains in South-Western Nigeria

Nigerian Journal of Animal Production ◽

10.51791/njap.v45i2.522 ◽

2020 ◽

Vol 45 (2) ◽

pp. 40-48

Author(s):

A. J. Atansuyi ◽

U. C. Ihendu ◽

C. A. Chineke

Keyword(s):

Body Weight ◽

Growth Performance ◽

Correlation Coefficients ◽

Tail Length ◽

Experimental Period ◽

The Body ◽

Coefficient Of Determination ◽

Indigenous Chicken ◽

Randomized Design ◽

Study Results

This study was conducted to determine the growth performance, correlation and regression estimates of seven-chicken strains in South-western Nigeria using a total of 300 day-old chicks. The birds were divided into seven groups based on their strain. The seven strains are Normal feather (NF), Fulani ecotype (FE), Frizzle feather (FF), naked neck (NN) and Transylvania indigenous strains while Hubbard and Marshal were meat-type exotic chickens. There were forty- five (45) unsexed day-old chicks in each strain except the Frizzle feather that were 30 in number. Completely randomized design (CRD) was used for the trial that lasted for 8 weeks. The birds were fed experimental diets ad libitum throughout the period of the study. Results showed that there were significant differences (p<0.05) in the initial and final weights of the birds. It was observed that exotic strains weighed heavier (3569.73gHB) than their indigenous counterparts (1391.11gNF). However, the Fulani ecotype weighed heaviest (1840.99g) among Nigeria indigenous strains during the experimental period. This showed that FE strains are generally heavy breed chicken and could be incorporated into a meat producing indigenous chicken if improved upon. The result of the correlation coefficients showed that a very strong, positive and highly significant (P<0.001) relationship existed between body weights and linear body measurements as most of the values are (>0.40). All the body parameter examined had significant (p<0.01) and direct relationship with the body weight. Shoulder-to-tail length (STL) had the highest coefficient of 0.98.The high correlation estimates obtained in this study could be as a result of pleiotropy, heterozygosity or linkage of genes in the birds. The three functions were highly significant (p<0.05) for all the parameters studied. This shows that the functions well described the parameters. On the basis of coefficient of determination (R ), the body weight of poultry birds at any age can be predicted most accurately with BRG using cubic function.

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