Mapping the bacterial ecology on the phyllosphere of grass hay and the potential hazards of soaking fodder for horse gut health

Mapping Intimacies ◽

10.1101/494799 ◽

2018 ◽

Author(s):

Meriel Moore-Colyer ◽

Annette Longland ◽

Pat Harris ◽

Susan Crosthwaite

Keyword(s):

Best Practice ◽

Variable Region ◽

Diversity Indices ◽

Water Soluble ◽

Soluble Carbohydrate ◽

Rrna Gene ◽

Gut Health ◽

Hygienic Quality ◽

Significant Difference ◽

Industry Practice

Globally hay is the preferred forage for stabled horses. Variable nutritional and hygienic quality stimulates pre-feeding soaking to reduce dust and nutrients to reduce respiratory and metabolic disorders in horses. However, this practice has potential negative impacts on horse health. The objectives of this study were to map the bacterial profile of different hays and determine how soaking alters this with the aim of recommending best practice when feeding fodder to stabled horses. Two meadow and one Perennial Ryegrass hays were soaked for 0, 1.5, 9 or 16 hours. Post treatment, hays were analysed for water-soluble carbohydrate (WSC) and total aerobic bacteria (TVC), with differences determined using ANOVA and least significant difference. Bacteria were identified via genomic DNA extraction (V3 and V4 variable region of the 16S rRNA gene) and 16S library preparation according to the Illumina protocol. Differences in phyla and family operational taxonomic units within hay types were identified via paired t-tests on the DESeq2 normalised data and false discovery rates accounted for using Padj (P<0.05). Mean WSC losses g/kg DM (+/- SE) increased with soaking time being 30 (10.7), 72 (43.7), 80 (38.8) for 1.5, 9 and 16 hours soak respectively. No relationship existed between WSC leaching and bacteria content or profile. Grass type influenced bacterial profiles. Soaking altered the epiphytic bacterial profile across all hays and 9 hours soaking increased richness and Shannon diversity indices. Clustering of bacteria was seen between meadow hays which differed from perennial rye grass and this difference increased post soaking. The normal industry practice of soaking hay for 9 hours pre-feeding cannot be recommended as it increases total bacteria content with noted increases of some potential pathogens. The alterations in bacteria profile and hygienic quality may explain why changing fodder or pre-feeding treatments can frequently precipitate colic in horses.

Gut bacterial microbiota in patients with myasthenia gravis: results from the MYBIOM study

Therapeutic Advances in Neurological Disorders ◽

10.1177/17562864211035657 ◽

2021 ◽

Vol 14 ◽

pp. 175628642110356

Author(s):

Andreas Totzeck ◽

Elakiya Ramakrishnan ◽

Melina Schlag ◽

Benjamin Stolte ◽

Kathrin Kizina ◽

...

Keyword(s):

Gut Microbiota ◽

Myasthenia Gravis ◽

Healthy Volunteers ◽

Alpha Diversity ◽

Diversity Indices ◽

Rrna Gene ◽

Pilot Studies ◽

Variable Regions ◽

Alpha And Beta Diversity ◽

Significant Difference

Background: Myasthenia gravis (MG) is an autoimmune neuromuscular disease, with gut microbiota considered to be a pathogenetic factor. Previous pilot studies have found differences in the gut microbiota of patients with MG and healthy individuals. To determine whether gut microbiota has a pathogenetic role in MG, we compared the gut microbiota of patients with MG with that of patients with non-inflammatory and inflammatory neurological disorders of the peripheral nervous system (primary endpoint) and healthy volunteers (secondary endpoint). Methods: Faecal samples were collected from patients with MG ( n = 41), non-inflammatory neurological disorder (NIND, n = 18), chronic inflammatory demyelinating polyradiculoneuropathy (CIDP, n = 6) and healthy volunteers ( n = 12). DNA was isolated from these samples, and the variable regions of the 16S rRNA gene were sequenced and statistically analysed. Results: No differences were found in alpha- and beta-diversity indices computed between the MG, NIND and CIDP groups, indicating an unaltered bacterial diversity and structure of the microbial community. However, the alpha-diversity indices, namely Shannon, Chao 1 and abundance-based coverage estimators, were significantly reduced between the MG group and healthy volunteers. Deltaproteobacteria and Faecalibacterium were abundant within the faecal microbiota of patients with MG compared with controls with non-inflammatory diseases. Conclusion: Although the overall diversity and structure of the gut microbiota did not differ between the MG, NIND and CIDP groups, the significant difference in the abundance of Deltaproteobacteria and Faecalibacterium supports the possible role of gut microbiota as a contributor to pathogenesis of MG. Further studies are needed to confirm these findings and to develop possible treatment strategies.

Selection of Lactic Acid Bacteria from Alfalfa Silage and Its Effects as Inoculant on Silage Fermentation

Agriculture ◽

10.3390/agriculture10110518 ◽

2020 ◽

Vol 10 (11) ◽

pp. 518

Author(s):

Vanessa P. Silva ◽

Odilon G. Pereira ◽

Eliana S. Leandro ◽

Rosinea A. Paula ◽

Mariele C. N. Agarussi ◽

...

Keyword(s):

Lactic Acid ◽

Lactic Acid Bacteria ◽

Ammonia Nitrogen ◽

Water Soluble ◽

Neutral Detergent Fiber ◽

Soluble Carbohydrate ◽

Rrna Gene ◽

Residual Water ◽

Lactobacillus Pentosus ◽

Alfalfa Silage

The first part of the study aimed to isolate, characterize, and identify wild lactic acid bacteria (LAB) strains from alfalfa silage produced in a tropical area. LAB strains were isolated from alfalfa silage ensiled for 1, 3, 7, 14, 28, and 56 days (d) and were identified by sequencing the 16S rRNA gene. The second part aimed to investigate the effects of wild LAB strains on the nutritive and fermentative characteristics of alfalfa silage. This trial was conducted according to a completely randomized design in a 4 × 2 factorial scheme [four inoculants (I) × two harvests (H)], (n = 4). The inoculants were: (1) no inoculant (CTRL), (2) Lactobacillus pentosus (AV 14.17); (3) L. pentosus + Lactobacillus brevis + Pediococcus acidilactici (Combo); and (4) commercial inoculant (CI). Alfalfa forage (7 kg) was ensiled in 10 L buckets and opened after 90 d. Seventy-seven strains were isolated. Pediococcus, Lactobacillus, and Weissella represented 52.0, 24.7, and 20.8% of the isolates, respectively. For the first harvest, Combo, CI, and all inoculated silages showed lower acid detergent fiber ADF, neutral detergent fiber (NDF), and ammonia nitrogen (NH3-N), respectively. Silage fermented with AV14.17 presented greater residual water-soluble carbohydrate (WSC) in the second harvest and showed the lowest pH in both harvests. AV14.17 strain has potential as an inoculant for alfalfa silage production.

PSIV-14 Fecal Microbiome of Horses Grazing Integrated Warm- and Cool-Season Grass Rotational Pasture Systems

Journal of Animal Science ◽

10.1093/jas/skaa278.499 ◽

2020 ◽

Vol 98 (Supplement_4) ◽

pp. 276-277

Author(s):

Jennifer R Weinert ◽

Amy S Biddle ◽

Carey A Williams

Keyword(s):

Random Forest ◽

Statistical Significance ◽

Random Forest Classifier ◽

Water Soluble ◽

Neutral Detergent Fiber ◽

Soluble Carbohydrates ◽

Soluble Carbohydrate ◽

Rrna Gene ◽

Microbial Composition ◽

Forage Type

Abstract The objective of this study was to characterize shifts in the fecal microbiota of horses grazing different forage types within integrated cool- and warm-season grass (CSG; WSG) pasture systems and to explore relationships between forage nutrients and microbial composition. Eight mares grazed integrated rotational systems containing mixed CSG and one of two WSG: bermudagrass or crabgrass. Fecal samples were collected after 2–3 weeks grazing WSG, CSG, and following an orchardgrass hay diet (HAY). Forage nutrients were determined by near-infrared spectroscopy and analyzed by two-way ANOVA in SAS (v.9.4). Following DNA extraction, 16S rRNA gene sequence analysis was conducted in QIIME 2 (v.2020.2) with Kruskall-Wallis tests for alpha diversity, Spearman correlation with forage nutrients, and taxonomic assignment with Greengenes. A random forest classifier and regressor determined ability to predict forage type and nutrients based upon bacterial composition. Statistical significance was set at p ≤ 0.05. Forage water-soluble carbohydrates (WSC) were greatest in CSG and lowest in WSG; neutral detergent fiber (NDF) was greater in HAY than CSG or WSG. Species richness and evenness (Shannon Index) was greater in horses adapted to WSG vs. CSG or HAY and was correlated with WSC (rs = -0.49) and ethanol-soluble carbohydrates (ESCrs = -0.62). The random forest classifier resulted in model accuracy of 1.0 and identified amplicon sequence variants (ASV) most important in prediction of forage type. Sixteen ASV were from the order Clostridiales including Lachnospiraceae, Ruminococcacceae, and Veillonellaceae families and the genus Coprococcus. Other important taxa included Prevotella spp., Streptococcus luteciae, and Fibrobacter succinogenes. The regressor accurately predicted WSC (r2 = 0.95) and ESC (r2 = 0.84), but not NDF (r2 = 0.09). These results suggest that the equine hindgut microbiome is impacted by forage type and soluble carbohydrate content; however, further research is required to determine functional and physiological significance in grazing horses.

Effects of ensilage of grass on performance and nutrient utilization by dairy cattle 1. Food intake and milk production

Animal Science ◽

10.1017/s1357729800013217 ◽

1995 ◽

Vol 60 (3) ◽

pp. 337-345 ◽

Cited By ~ 13

Author(s):

A. Cushnahan ◽

C. S. Mayne

Keyword(s):

Dry Matter ◽

Nitrogen Concentration ◽

Nutrient Utilization ◽

Milk Composition ◽

Ammonia Nitrogen ◽

Period Change ◽

Water Soluble ◽

Soluble Carbohydrate ◽

Carbohydrate Concentration ◽

Significant Difference

AbstractTwelve lactatiug dairy cows were offered either fresh grass (G) or grass silage prepared from the same pasture which had undergone either an extensive (E) or restricted (R) fermentation, in a three-period change-over design experiment. Ensilage resulted in a reduction in forage pH and water-soluble carbohydrate concentration and an increase in ammonia-nitrogen concentration. The ensiling techniques used ensured that both silages were well preserved with pH values for E and R of 3.81 and 4.08 respectively, while the respective lactic acid concentrations were 124.6 and 27.0 g/kg dry matter respectively. Whilst there were no significant differences in dry-matter intake between treatments, when corrected for losses of volatile compounds, animals offered silage with a restricted fermentation consumed their food at a higher rate of intake (P < 0.001) than did animals on the other treatments. It was also found that while there was no significant difference in milk yield between animals offered fresh or ensiled forage, both butterfat and protein concentration and yields of butterfat were significantly higher (P < 0.01 or greater) with grass and restricted fermented silage than with extensively fermented silage. Ensiling of herbage had no significant effect on apparent digestibility. It is concluded that ensiling of herbage per se had little effect on overall animal performance but pattern of silage fermentation resulted in alterations in milk composition.

Meta-analysis of bovine respiratory microbiota: link between respiratory microbiota and bovine respiratory health

FEMS Microbiology Ecology ◽

10.1093/femsec/fiaa127 ◽

2020 ◽

Vol 96 (8) ◽

Author(s):

Mohamed Zeineldin ◽

Ahmed A. Elolimy ◽

Radwa Barakat

Keyword(s):

16S Rrna ◽

Respiratory Tract ◽

Respiratory Health ◽

Meta Analysis ◽

Hypervariable Region ◽

Diversity Indices ◽

Feedlot Cattle ◽

Rrna Gene ◽

Significant Difference ◽

Respiratory Microbiota

ABSTRACT Bovine respiratory microbiota plays a significant role in bovine respiratory health. We conducted a meta-analysis using publicly available 16S rRNA gene datasets from the respiratory tract to characterize respiratory microbiota in feedlot cattle. Our aims were to determine the factors that influence microbiota development and to assess the differences in microbiota composition and diversity between healthy calves and those that developed bovine respiratory disease (BRD). Our results showed that the overall composition and diversity of respiratory microbiota in cattle were significantly affected by study design, 16S rRNA hypervariable region sequenced, health status, time since arrival to the feedlot, sampling sites in the respiratory tract and antibiotic treatment. Assessment of diversity indices showed a statistically significant difference between the BRD-affected cattle and healthy control calves. Using multivariate network analysis and Spearman's correlation analyses, we further distinguished the taxa that were commonly associated with BRD when the day of arrival to the feedlot was added to the model. The probability of being identified as BRD was significantly correlated with days 7, 12 and 14 following the calf's arrival to the feedlot. These findings could help in proposing strategies to further evaluate the link between respiratory microbiota and bovine respiratory health.

Modulation of Gut Microbiota in Korean Navy Trainees following a Healthy Lifestyle Change

Microorganisms ◽

10.3390/microorganisms8091265 ◽

2020 ◽

Vol 8 (9) ◽

pp. 1265

Author(s):

YeonGyun Jung ◽

Setu Bazie Tagele ◽

HyunWoo Son ◽

Jerald Conrad Ibal ◽

Dorsaf Kerfahi ◽

...

Keyword(s):

Alcohol Consumption ◽

Physical Exercise ◽

Gut Microbiota ◽

Healthy Lifestyle ◽

Variable Region ◽

Lifestyle Factors ◽

Rrna Gene ◽

Gut Flora ◽

Α Diversity ◽

Significant Difference

Environmental factors can influence the composition of gut microbiota, but understanding the combined effect of lifestyle factors on adult gut microbiota is limited. Here, we investigated whether changes in the modifiable lifestyle factors, such as cigarette smoking, alcohol consumption, sleep duration, physical exercise, and body mass index affected the gut microbiota of Korean navy trainees. The navy trainees were instructed to stop smoking and alcohol consumption and follow a sleep schedule and physical exercise regime for eight weeks. For comparison, healthy Korean civilians, who had no significant change in lifestyles for eight weeks were included in this study. A total of 208 fecal samples were collected from navy trainees (n = 66) and civilians (n = 38) at baseline and week eight. Gut flora was assessed by sequencing the highly variable region of the 16S rRNA gene. The α-and β -diversity of gut flora of both the test and control groups were not significantly changed after eight weeks. However, there was a significant difference among individuals. Smoking had a significant impact in altering α-diversity. Our study showed that a healthy lifestyle, particularly cessation of smoking, even in short periods, can affect the gut microbiome by enhancing the abundance of beneficial taxa and reducing that of harmful taxa.

Campylobacter jejuni transmission and colonisation in broiler chickens is inhibited by Faecal Microbiota Transplantation

10.1101/476119 ◽

2018 ◽

Cited By ~ 2

Author(s):

Rachel Gilroy ◽

Gemma Chaloner ◽

Amy Wedley ◽

Lizeth Lacharme-Lora ◽

Sue Jopson ◽

...

Keyword(s):

Campylobacter Jejuni ◽

Human Infection ◽

Intestinal Microbiome ◽

Infection Model ◽

Rrna Gene ◽

Broiler Chicks ◽

Gut Health ◽

Faecal Microbiota ◽

Intestinal Colonisation ◽

Significant Difference

ABSTRACTBACKGROUNDCampylobacter jejuni, the most frequent cause of foodborne bacterial infection, is found on around 70% of retail chicken. As such there is a need for effective controls in chicken production. Microbial-based controls such as probiotics are attractive to the poultry industry, but of limited efficacy. Furthermore, as commercially-produced chickens have no maternal contact, their pioneer microbiome is likely to come from the hatchery environment. Early delivery of microbials that lead to a more ‘natural avian’ microbiome may, therefore, improve bird health and reduce susceptibility to C.jejuni colonisation.A faecal microbiota transplant (FMT) was used to transfer a mature cecal microbiome to newly-hatched broiler chicks and its effects on C.jejuni challenge assessed. We used both a seeder-bird infection model that mimics natural bird-to-bird infection alongside a direct-challenge model. We used a 16S rRNA gene sequencing-based approach to characterize the transplant material itself alongside changes to the chicken microbiome following FMT.RESULTSFMT changes the composition of the chicken intestinal microbiome. We observed little change in species richness following FMT compared to untreated samples, but there is an increase in phylogenetic diversity within those species. The most significant difference in the ceca is an increase in Lactobacilli, although not a major component of the transplant material, suggesting the FMT results in a change in the intestinal milieu as much as a direct change to the microbiome.Upon direct challenge, FMT resulted in lower initial intestinal colonisation with C.jejuni. More significantly, in a seeder-bird challenge of infection transmission, FMT reduced transmission and intestinal colonisation until common UK retail age of slaughter. In a repeat experiment, transmission was completely blocked following FMT treatment. Delayed FMT administration at 7 days of-age had limited effect on colonisation and transmission.CONCLUSIONSWe show that transfer of a whole mature microbiome to newly-hatched chicks reduces transmission and colonisation of C.jejuni. This indicates that modification of the broiler chick microbiome can reduce intestinal colonisation of C.jejuni to levels projected to lead to lower the human infection rate. We believe these findings offer a way to identify key taxa or consortia that are effective in reducing C.jejuni colonisation and improving broiler gut health.

Gut microbiota of endangered crested ibis: Establishment, diversity, and association with reproductive output

PLoS ONE ◽

10.1371/journal.pone.0250075 ◽

2021 ◽

Vol 16 (4) ◽

pp. e0250075

Author(s):

Jian Ran ◽

Qiu-Hong Wan ◽

Sheng-Guo Fang

Keyword(s):

Gut Microbiota ◽

Alpha Diversity ◽

16S Rrna Gene Sequencing ◽

Diversity Indices ◽

Reproductive Capacity ◽

Rrna Gene ◽

Alpha And Beta Diversity ◽

Microbiome Composition ◽

Crested Ibis ◽

Significant Difference

Gut microbiota is known to influence the host’s health; an imbalance of the gut microbial community leads to various intestinal and non-intestinal diseases. Research on gut microbes of endangered birds is vital for their conservation. However, a thorough understanding of the gut microbiome composition present in crested ibises at different ages and its correlation with crested ibis reproductive capacity has remained elusive. Here, we used 16S rRNA gene sequencing to explore the fecal microbial structure of nestlings and adult birds, and the difference in gut microbiota between healthy and sterile crested ibises. We observed that (1) bacterial microbiota, alpha and beta diversity of one-day-old nestlings significantly distinguished from other nestlings; abundance of Proteobacteria decreased, while that of Fusobacteria increased with an increase in the age of the nestlings; (2) there was no significant difference in community composition among adult crested ibises aged one, two, three, and five years; (3) the abundance of Proteobacteria and alpha diversity indices were higher in sterile crested ibises than in healthy crested ibises; thus, Proteobacteria can act as a diagnostic biomarker of reproductive dysfunction in crested ibises. This study significantly contributes to the field of ecology and conservation, as it provides a platform for assessing the reproductive capacity of endangered crested ibises, based on the gut microbiota composition. Further studies may unravel additional factors influencing crested ibises’ reproductive health, which will further help the management and control of the crested ibis population.

Diversity, Composition and Functional Inference of Gut Microbiota in Indian Cabbage white Pieris canidia (Lepidoptera: Pieridae)

Life ◽

10.3390/life10110254 ◽

2020 ◽

Vol 10 (11) ◽

pp. 254

Author(s):

Ying Wang ◽

Jianqing Zhu ◽

Jie Fang ◽

Li Shen ◽

Shuojia Ma ◽

...

Keyword(s):

Gut Microbiota ◽

16S Rrna Gene Sequencing ◽

Adult Survival ◽

Rrna Gene ◽

Life Stages ◽

Microbial Composition ◽

Significant Difference ◽

Functional Inference ◽

Rrna Gene Sequencing ◽

Insect Fitness

We characterized the gut microbial composition and relative abundance of gut bacteria in the larvae and adults of Pieris canidia by 16S rRNA gene sequencing. The gut microbiota structure was similar across the life stages and sexes. The comparative functional analysis on P. canidia bacterial communities with PICRUSt showed the enrichment of several pathways including those for energy metabolism, immune system, digestive system, xenobiotics biodegradation, transport, cell growth and death. The parameters often used as a proxy of insect fitness (development time, pupation rate, emergence rate, adult survival rate and weight of 5th instars larvae) showed a significant difference between treatment group and untreated group and point to potential fitness advantages with the gut microbiomes in P. canidia. These data provide an overall view of the bacterial community across the life stages and sexes in P. canidia.

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

Journal of Animal Science ◽

10.1093/jas/skaa278.729 ◽

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.