Resilience of Faecal Microbiota in Stabled Thoroughbred Horses Following Abrupt Dietary Transition between Freshly Cut Pasture and Three Forage-Based Diets

The management of competition horses in New Zealand often involves rotations of short periods of stall confinement and concentrate feeding, with periods of time at pasture. Under these systems, horses may undergo abrupt dietary changes, with the incorporation of grains or concentrate feeds to the diet to meet performance needs, or sudden changes in the type of forage fed in response to a lack of fresh or conserved forage. Abrupt changes in dietary management are a risk factor for gastrointestinal (GI) disturbances, potentially due to the negative effects observed on the population of GI microbiota. In the present study, the faecal microbiota of horses was investigated to determine how quickly the bacterial communities; (1) responded to dietary change, and (2) stabilised following abrupt dietary transition. Six Thoroughbred mares were stabled for six weeks, consuming freshly cut pasture (weeks 1, 3 and 5), before being abruptly transitioned to conserved forage-based diets, both offered ad libitum. Intestinal markers were administered to measure digesta transit time immediately before each diet change. The conserved forage-based diets were fed according to a 3 × 3 Latin square design (weeks 2, 4 and 6), and comprised a chopped ensiled forage fed exclusively (Diet FE) or with whole oats (Diet FE + O), and perennial ryegrass hay fed with whole oats (Diet H + O). Faecal samples were collected at regular intervals from each horse following the diet changes. High throughput 16S rRNA gene sequencing was used to evaluate the faecal microbiota. There were significant differences in alpha diversity across diets (p < 0.001), and a significant effect of diet on the beta diversity (ANOSIM, p = 0.001), with clustering of samples observed by diet group. There were differences in the bacterial phyla across diets (p < 0.003), with the highest relative abundances observed for Firmicutes (62–64%) in the two diets containing chopped ensiled forage, Bacteroidetes (32–38%) in the pasture diets, and Spirochaetes (17%) in the diet containing hay. Major changes in relative abundances of faecal bacteria appeared to correspond with the cumulative percentage of intestinal markers retrieved in the faeces as the increasing amounts of digesta from each new diet transited the animals. A stable faecal microbiota profile was observed in the samples from 96 h after abrupt transition to the treatment diets containing ensiled chopped forage. The present study confirmed that the diversity and community structure of the faecal bacteria in horses is diet-specific and resilient following dietary transition and emphasised the need to have modern horse feeding management that reflects the ecological niche, particularly by incorporating large proportions of forage into equine diets.

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Gut Microbiome Changes in Captive Plateau Zokors (Eospalax baileyi)

Evolutionary Bioinformatics ◽

10.1177/1176934321996353 ◽

2021 ◽

Vol 17 ◽

pp. 117693432199635

Author(s):

Daoxin Liu ◽

Pengfei Song ◽

Jingyan Yan ◽

Haijing Wang ◽

Zhenyuan Cai ◽

...

Keyword(s):

Gut Microbiota ◽

Gut Microbiome ◽

High Throughput Sequencing ◽

Tibet Plateau ◽

Rrna Gene ◽

Diversity Analysis ◽

Bacterial Phyla ◽

In Captivity ◽

Relative Abundances ◽

Plateau Zokor

Wild-caught animals must cope with drastic lifestyle and dietary changes after being induced to captivity. How the gut microbiome structure of these animals will change in response receives increasing attention. The plateau zokor ( Eospalax baileyi), a typic subterranean rodent endemic to the Qinghai-Tibet plateau, spends almost the whole life underground and is well adapted to the environmental pressures of both plateau and underground. However, how the gut microbiome of the plateau zokor will change in response to captivity has not been reported to date. This study compared the microbial community structure and functions of 22 plateau zokors before (the WS group) and after being kept in captivity for 15 days (the LS group, fed on carrots) using the 16S rRNA gene via high-throughput sequencing technology. The results showed that the LS group retained 973 of the 977 operational taxonomic units (OTUs) in the WS group, and no new OTUs were found in the LS group. The dominant bacterial phyla were Bacteroides and Firmicutes in both groups. In alpha diversity analysis, the Shannon, Sobs, and ACE indexes of the LS group were significantly lower than those of the WS group. A remarkable difference ( P < 0.01) between groups was also detected in beta diversity analysis. The UPGMA clustering, NMDS, PCoA, and Anosim results all showed that the intergroup difference was significantly greater than the intragroup difference. And compared with the WS group, the intragroup difference of the gut microbiota in the LS group was much larger, which failed to support the assumption that similar diets should drive convergence of gut microbial communities. PICRUSt revealed that although some functional categories displayed significant differences between groups, the relative abundances of these categories were very close in both groups. Based on all the results, we conclude that as plateau zokors enter captivity for a short time, although the relative abundances of different gut microbiota categories shifted significantly, they can maintain almost all the OTUs and the functions of the gut microbiota in the wild. So, the use of wild-caught plateau zokors in gut microbial studies is acceptable if the time in captivity is short.

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A contribution to the larval amphibian microbiome: characterization of bacterial microbiome of Ichthyophis bannanicus (Order: Gymnophiona) and comparison with the other two amphibian orders

10.1101/2021.09.20.461075 ◽

2021 ◽

Author(s):

Amrapali Rajput ◽

Shipeng Zhou ◽

Madhava Meegaskumbura

Keyword(s):

Gut Microbiome ◽

Alpha Diversity ◽

The Other ◽

Rrna Gene ◽

Scaling Analysis ◽

Skin Microbiome ◽

Sequencing Platform ◽

Bacterial Phyla ◽

Faecal Samples ◽

Skin Samples

It is known that animal-associated microbiomes form indispensable relationships with hosts and are responsible for many functions important for host-survival. Next-gen driven approaches documenting the remarkable diversity of microbiomes have burgeoned, with amphibians too, benefiting from such treatments. The microbiome of Gymnophiona (caecilians), one of the three amphibian orders, constituting of 3% of amphibians, however, remains almost unknown. The present study aims to address this knowledge gap through analysis of the microbiome of Ichthyophis bannanicus. As these caecilian larvae are aquatic and hence exposed to a greater propensity for bacterial microbiomic interchange, we hypothesize that bacterial phyla would overlap between gut and skin. Further, from the host-specificity patterns observed in other vertebrate taxa, we hypothesize that Gymnophiona have different dominant gut bacterial microbiomes at a higher taxonomic level when compared to the larvae of the other two amphibian orders (Anura and Caudata). We used 16S rRNA gene amplicon sequencing based on Illumina Nova sequencing platform to characterize and compare the gut (represented by faecal samples) and skin microbiome of I. bannanicus larvae (N = 13), a species distributed across South-East-Asia and the only caecilian species occurring in China. We compared our gut microbiome results with published anuran and caudate larval microbiomes. For I. bannanicus, a total of 4,053 operational taxonomic units (OTU) across 13 samples were detected. Alpha-diversity indices were significant between gut and skin samples. Non-metric multidimensional scaling analysis suggest that gut and skin samples each contained a distinct microbiome at OTU level. We record significant differences between the bacterial phyla of gut and skin samples in larvae of I. bannanicus. The study provides an overview of gut and skin bacterial microbiomes of a caecilian, while highlighting the major differences between larval microbiomes of the three amphibian orders. We find a partial overlap of gut bacterial microbiomes at phylum level for the three orders; however, the relative abundance of the dominant phyla is distinct. The skin and gut microbiomes are distinct with little overlap of species, highlighting that gut-skin axis is weak. This in turn suggests that many of the microbial species on skin and gut are functionally specialized to those locations. We also show that the skin microbiome is more diverse than the gut microbiome at species level; however, a reason for this could be a portion of the gut microbiome not being represented in faecal samples. These first microbiome information from a caecilian lay the foundation for comparative studies of the three amphibian orders.

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Housing conditions, level of feeding and presence of antibiotics in the feed shape rabbit cecal microbiota

10.21203/rs.3.rs-38388/v3 ◽

2020 ◽

Author(s):

María Velasco-Galilea ◽

Miriam Guivernau ◽

Miriam Piles ◽

Marc Viñas ◽

Oriol Rafel ◽

...

Keyword(s):

Alpha Diversity ◽

Rrna Gene ◽

Housing Conditions ◽

Animal Performance ◽

Production Environment ◽

Feed Composition ◽

Animal Management ◽

Cecal Microbiota ◽

Relative Abundances ◽

The Impact

Abstract Background: the effect of the production environment and different management practices in rabbit cecal microbiota remains poorly understood. While previous studies have proved the impact of the age or the feed composition, research in the housing conditions and other animal management aspects, such as the presence of antibiotics in the feed or the level of feeding, is still needed. Characterization of microbial diversity and composition of growing rabbits raised under different conditions could help better understand the role these practices play in cecal microbial communities and how it may result in different animal performance.Results: four hundred twenty-five meat rabbits raised in two different facilities, fed under two feeding regimes (ad libitum or restricted) with feed supplemented or free of antibiotics, were selected for this study. A 16S rRNA gene-based assessment through the MiSeq Illumina sequencing platform was performed on cecal samples collected from these individuals at slaughter. Different univariate and multivariate approaches were conducted to unravel the influence of the different factors on microbial alpha diversity and composition at phylum, genus and OTU taxonomic levels. The animals raised in the facility harboring the most stable environmental conditions had greater, and less variable, microbial richness and diversity. Bootstrap univariate analyses of variance and sparse partial least squares-discriminant analyses endorsed that farm exerted the largest influence on rabbit microbiota since the relative abundances of many taxa were found differentially represented between both facilities at all taxonomic levels characterized. Furthermore, only five OTUs were needed to achieve a perfect classification of samples according to the facility where animals were raised. The level of feeding and the presence of antibiotics did not modify the global alpha diversity but had an impact on some bacteria relative abundances, albeit in a small number of taxa compared with farm, which is consistent with the lower sample classification power according to these factors achieved using microbial information.Conclusions: this study reveals different degrees of influence attributable to environment and animal management. It highlights the importance of offering a controlled breeding environment that reduces differences in microbial cecal composition that could be causative of different animal performance.

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Effects of Smoking and Smoking Cessation on the Intestinal Microbiota

Journal of Clinical Medicine ◽

10.3390/jcm9092963 ◽

2020 ◽

Vol 9 (9) ◽

pp. 2963

Author(s):

Marcus G. Sublette ◽

Tzu-Wen L. Cross ◽

Claudia E. Korcarz ◽

Kristin M. Hansen ◽

Sofia M. Murga-Garrido ◽

...

Keyword(s):

Smoking Cessation ◽

Intestinal Microbiota ◽

Disease Risk ◽

Cardiovascular Disease Risk ◽

Alpha Diversity ◽

16S Rrna Gene Sequencing ◽

Rrna Gene ◽

Alpha And Beta Diversity ◽

Quit Attempt ◽

Relative Abundances

We evaluated associations of smoking heaviness markers and the effects of smoking cessation on the intestinal microbiota and cardiovascular disease risk factors in current smokers undertaking a quit attempt. Participants were current smokers enrolled in a prospective randomized clinical trial of smoking cessation therapies with visits at baseline, 2, and 12 weeks. Genomic DNA was extracted from fecal samples followed by 16S rRNA gene sequencing and analysis using the QIIME2 software workflow. Relative abundances of bacterial taxa and alpha- and beta-diversity measures were used for comparisons. The 36 smokers were (mean (standard deviation)) 51.5 (11.1) years old (42% male) and smoked 15.1 (6.4) cigarettes per day for 22.7 (11.9) pack-years. Relative abundances of the phylum Actinobacteria correlated with pack-years (rho = −0.44, p = 0.008) and Cyanobacteria correlated with CO levels (rho = 0.39, p = 0.021). After 12 weeks, relative abundances of the phylum Bacteroidetes increased (pANCOVA = 0.048) and Firmicutes decreased (pANCOVA = 0.036) among abstainers compared to continuing smokers. Increases in alpha-diversity were associated with heart rates (rho = −0.59, p = 0.037), systolic blood pressures (rho = −0.58, p = 0.043), and C-reactive protein (rho = −0.60, p = 0.034). Smoking cessation led to minor changes in the intestinal microbiota. It is unclear if the proven health benefits of smoking cessation lead to salutary changes in the intestinal microbiota.

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Fecal microbiota in untreated children with Juvenile Idiopathic Arthritis – a comparison with healthy children and healthy siblings

The Journal of Rheumatology ◽

10.3899/jrheum.200551 ◽

2020 ◽

pp. jrheum.200551

Author(s):

Anders Öman ◽

Johan Dicksved ◽

Lars Engstrand ◽

Lillemor Berntson

Keyword(s):

Juvenile Idiopathic Arthritis ◽

Community Composition ◽

Alpha Diversity ◽

Fecal Microbiota ◽

Rrna Gene ◽

Healthy Children ◽

Healthy Controls ◽

Α Diversity ◽

Healthy Siblings ◽

Relative Abundances

Objective Changes in the composition of gut microbiota has been suggested to be associated with Juvenile idiopathic arthritis (JIA). The objective in this study was to investigate if the diversity and composition of the fecal microbiota differed between children with JIA and healthy controls, and if the microbiota differed between children with JIA and their healthy siblings. Methods In this multicenter, case-control study, fecal samples were collected from 75 children with JIA and 32 healthy controls. Eight of the healthy controls were siblings to eight children with JIA and they were compared only pairwise with their siblings. The microbiota was determined using sequencing amplicons from the V3 and V4 regions of the 16S rRNA gene. Alpha diversity, community composition of microbiota and relative abundances of taxa were compared between children with JIA and healthy unrelated controls as well as between children with JIA and healthy siblings. Results Our data revealed no significant differences in α-diversity or community composition of microbiota between children with JIA, healthy unrelated controls or healthy siblings. Analyses of relative abundances of phyla, families and genera identified trends of differing abundances of some taxa in children with JIA, in comparison with both healthy controls and healthy siblings, but none of these findings were significant after adjustment for multiple comparisons. Conclusion There were no significant differences in the composition of fecal microbiota in children with JIA compared with healthy controls. The composition of microbiota in children with JIA did not differ significantly from that in their healthy siblings.

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Breeding farm, level of feeding and presence of antibiotics in the feed influence rabbit cecal microbiota

Animal Microbiome ◽

10.1186/s42523-020-00059-z ◽

2020 ◽

Vol 2 (1) ◽

Author(s):

María Velasco-Galilea ◽

Miriam Guivernau ◽

Miriam Piles ◽

Marc Viñas ◽

Oriol Rafel ◽

...

Keyword(s):

Microbial Communities ◽

Management Practices ◽

Alpha Diversity ◽

Rrna Gene ◽

Animal Performance ◽

Production Environment ◽

Feed Composition ◽

Cecal Microbiota ◽

Relative Abundances ◽

The Impact

Abstract Background The effect of the production environment and different management practices in rabbit cecal microbiota remains poorly understood. While previous studies have proved the impact of the age or the feed composition, research in the breeding farm and other animal management aspects, such as the presence of antibiotics in the feed or the level of feeding, is still needed. Characterization of microbial diversity and composition of growing rabbits raised under different conditions could help better understand the role these practices play in cecal microbial communities and how it may result in different animal performance. Results Four hundred twenty-five meat rabbits raised in two different facilities, fed under two feeding regimes (ad libitum or restricted) with feed supplemented or free of antibiotics, were selected for this study. A 16S rRNA gene-based assessment through the MiSeq Illumina sequencing platform was performed on cecal samples collected from these individuals at slaughter. Different univariate and multivariate approaches were conducted to unravel the influence of the different factors on microbial alpha diversity and composition at phylum, genus and OTU taxonomic levels. The animals raised in the facility harboring the most stable environmental conditions had greater, and less variable, microbial richness and diversity. Bootstrap univariate analyses of variance and sparse partial least squares-discriminant analyses endorsed that farm conditions exerted an important influence on rabbit microbiota since the relative abundances of many taxa were found differentially represented between both facilities at all taxonomic levels characterized. Furthermore, only five OTUs were needed to achieve a perfect classification of samples according to the facility where animals were raised. The level of feeding and the presence of antibiotics did not modify the global alpha diversity but had an impact on some bacteria relative abundances, albeit in a small number of taxa compared with farm, which is consistent with the lower sample classification power according to these factors achieved using microbial information. Conclusions This study reveals that factors associated with the farm effect and other management factors, such as the presence of antibiotics in the diet or the feeding level, modify cecal microbial communities. It highlights the importance of offering a controlled breeding environment that reduces differences in microbial cecal composition that could be responsible for different animal performance.

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Effects of supplementing geese with green sweet sorghum stalks on microbiota in segments of the gastrointestinal tract

South African Journal of Animal Science ◽

10.4314/sajas.v50i3.9 ◽

2020 ◽

Vol 50 (3) ◽

pp. 421-433

Author(s):

H. Zhong ◽

Z. Liu ◽

M. Liang ◽

Q. Wang ◽

Y. Wang ◽

...

Keyword(s):

Gastrointestinal Tract ◽

Sweet Sorghum ◽

Endocrine System ◽

Alpha Diversity ◽

Basal Diet ◽

Diet Group ◽

Rrna Gene ◽

Intestinal Segments ◽

Group 2 ◽

Group 1

To explore the effects of supplementing a basal diet with green sweet sorghum stalks on the gut microbiota in geese, one hundred and twenty 28 day old geese were divided into two groups. Group 1 was fed a basal diet and group 2 was fed 92% of the same basal diet with green sweet sorghum stalks ad libitum for 42 days. Three male geese from each group were killed at 70 days old, four gastrointestinal tract segments (duodenum, jejunum, ileum, and caecum) were collected, and the hypervariable V4 region of the bacterial 16S rRNA gene was sequenced. There were obvious changes of microbiome in the caecum compared with the other three intestinal segments after green sweet sorghum stalks were added to the diet. Group 2 had significantly higher alpha diversity in the caecum compared with group 1 (P <0.05). The phyla of bacterial communities in the caecum differed. Group 2 had more abundant Bacteroidetes and Firmicutes, but Proteobacteria were more abundant in group 1. At genus level, Bacteroides was more prevalent in group 2, as were Prevotella and YRC22 (P <0.05). Functional analysis revealed that the carbohydrate metabolism, membrane transport, endocrine system and digestive system metabolic pathways were overrepresented in group 2. In conclusion, caecal microbes might play an important role in digesting green sweet sorghum stalks in geese.Keywords: caecum, goose, microbiome, microbial diversity

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In four shallow and mesophotic tropical reef sponges from Guam the microbial community largely depends on host identity

PeerJ ◽

10.7717/peerj.1936 ◽

2016 ◽

Vol 4 ◽

pp. e1936 ◽

Cited By ~ 31

Author(s):

Georg Steinert ◽

Michael W. Taylor ◽

Peter Deines ◽

Rachel L. Simister ◽

Nicole J. de Voogd ◽

...

Keyword(s):

Environmental Factors ◽

Beta Diversity ◽

Alpha Diversity ◽

Local Area ◽

Rrna Gene ◽

Bacterial Phyla ◽

Deep Reef ◽

Host Identity ◽

Tropical Reef ◽

Seawater Samples

Sponges (phylum Porifera) are important members of almost all aquatic ecosystems, and are renowned for hosting often dense and diverse microbial communities. While the specificity of the sponge microbiota seems to be closely related to host phylogeny, the environmental factors that could shape differences within local sponge-specific communities remain less understood. On tropical coral reefs, sponge habitats can span from shallow areas to deeper, mesophotic sites. These habitats differ in terms of environmental factors such as light, temperature, and food availability, as well as anthropogenic impact. In order to study the host specificity and potential influence of varying habitats on the sponge microbiota within a local area, four tropical reef sponges,Rhabdastrella globostellata,Callyspongiasp.,Rhaphoxyasp., andAcanthella cavernosa, were collected from exposed shallow reef slopes and a deep reef drop-off. Based on 16S rRNA gene pyrosequencing profiles, beta diversity analyses revealed that each sponge species possessed a specific microbiota that was significantly different to those of the other species and exhibited attributes that are characteristic of high- and/or low-microbial-abundance sponges. These findings emphasize the influence of host identity on the associated microbiota. Dominant sponge- and seawater-associated bacterial phyla were Chloroflexi, Cyanobacteria, and Proteobacteria. Comparison of individual sponge taxa and seawater samples between shallow and deep reef sites revealed no significant variation in alpha diversity estimates, while differences in microbial beta diversity (variation in community composition) were significant forCallyspongiasp. sponges and seawater samples. Overall, the sponge-associated microbiota is significantly shaped by host identity across all samples, while the effect of habitat differentiation seems to be less predominant in tropical reef sponges.

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Amazonia Seasons Have an Influence in the Composition of Bacterial Gut Microbiota of Mangrove Oysters (Crassostrea gasar)

Frontiers in Genetics ◽

10.3389/fgene.2020.602608 ◽

2021 ◽

Vol 11 ◽

Author(s):

Marcos Vinícius Reis Conceição ◽

Sávio Souza Costa ◽

Ana Paula Schaan ◽

Ândrea Kely Campos Ribeiro-dos-Santos ◽

Artur Silva ◽

...

Keyword(s):

Gut Microbiota ◽

Alpha Diversity ◽

16S Rrna Gene Sequencing ◽

Illumina Miseq ◽

Rrna Gene ◽

Sampling Effort ◽

Bacterial Composition ◽

Bacterial Phyla ◽

Close Relationship ◽

Crassostrea Corteziensis

The mangrove oysters (Crassostrea gasar) are molluscs native to the Amazonia region and their exploration and farming has increased considerably in recent years. These animals are farmed on beds built in the rivers of the Amazonia estuaries and, therefore, the composition of their microbiome should be directly influenced by environmental conditions. Our work aimed to evaluate the changes in bacterial composition of oyster's microbiota at two different seasons (rainy and dry). For this purpose, we amplified and sequenced the V3-V4 regions of the 16S rRNA gene. Sequencing was performed on the Illumina MiSeq platform. According to the rarefaction curve, the sampling effort was sufficient to describe the bacterial diversity in the samples. Alpha-diversity indexes showed that the bacterial microbiota of oysters is richer during the rainy season. This richness is possibly associated with the diversity at lower taxonomic levels, since the relative abundance of bacterial phyla in the two seasons remained relatively constant. The main phyla found include Firmicutes, Bacteroidetes, Actinobacteria, and Proteobacteria. Similar results were found for the species Crassostrea gigas, Crassostrea sikamea, and Crassostrea corteziensis. Beta-diversity analysis showed that the bacterial composition of oyster's gut microbiota was quite different in the two seasons. Our data demonstrate the close relationship between the environment and the microbiome of these molluscs, reinforcing the need for conservation and sustainable management of estuaries in the Amazonia.

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

BMC Veterinary Research ◽

10.1186/s12917-021-02994-8 ◽

2021 ◽

Vol 17 (1) ◽

Author(s):

Xiao Bin Li ◽

Xin Xin Huang ◽

Chang Jiang Zang ◽

Chen Ma ◽

Kai Xu Chen ◽

...

Keyword(s):

Body Weight ◽

Growth Performance ◽

Relative Abundance ◽

Alpha Diversity ◽

The Body ◽

Rrna Gene ◽

Faecal Microbiota ◽

Microbial Composition ◽

Faecal Samples ◽

Health And Development

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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