scholarly journals Development of the equine hindgut microbiome in semi-feral and domestic conventionally-managed foals

2020 ◽  
Vol 2 (1) ◽  
Author(s):  
Meredith K. Tavenner ◽  
Sue M. McDonnell ◽  
Amy S. Biddle
Keyword(s):  
Lactic Acid ◽  
Lactic Acid Bacteria ◽  
Gut Microbiome ◽  
Feral Horses ◽  
Microbiome Diversity ◽  
Rrna Sequencing ◽  
Domestic Horses ◽  
Species Groups ◽  
The Impact ◽  
Bacterial Groups

Abstract Background Early development of the gut microbiome is an essential part of neonate health in animals. It is unclear whether the acquisition of gut microbes is different between domesticated animals and their wild counterparts. In this study, fecal samples from ten domestic conventionally managed (DCM) Standardbred and ten semi-feral managed (SFM) Shetland-type pony foals and dams were compared using 16S rRNA sequencing to identify differences in the development of the foal hindgut microbiome related to time and management. Results Gut microbiome diversity of dams was lower than foals overall and within groups, and foals from both groups at Week 1 had less diverse gut microbiomes than subsequent weeks. The core microbiomes of SFM dams and foals had more taxa overall, and greater numbers of taxa within species groups when compared to DCM dams and foals. The gut microbiomes of SFM foals demonstrated enhanced diversity of key groups: Verrucomicrobia (RFP12), Ruminococcaceae, Fusobacterium spp., and Bacteroides spp., based on age and management. Lactic acid bacteria Lactobacillus spp. and other Lactobacillaceae genera were enriched only in DCM foals, specifically during their second and third week of life. Predicted microbiome functions estimated computationally suggested that SFM foals had higher mean sequence counts for taxa contributing to the digestion of lipids, simple and complex carbohydrates, and protein. DCM foal microbiomes were more similar to their dams in week five and six than were SFM foals at the same age. Conclusions This study demonstrates the impact of management on the development of the foal gut microbiome in the first 6 weeks of life. The higher numbers of taxa within and between bacterial groups found in SFM dams and foals suggests more diversity and functional redundancy in their gut microbiomes, which could lend greater stability and resiliency to these communities. The colonization of lactic acid bacteria in the early life of DCM foals suggests enrichment in response to the availability of dams’ feed. Thus, management type is an important driver of gut microbiome establishment on horses, and we may look to semi-feral horses for guidance in defining a healthy gut microbiome for domestic horses.

scholarly journals Development of the Equine Hindgut Microbiome in Semi-feral and Domestic Conventionally-Managed Foals

2020 ◽  
Author(s):  
Meredith Tavenner ◽  
Sue M McDonnell ◽  
Amy S Biddle
Keyword(s):  
Lactic Acid ◽  
Lactic Acid Bacteria ◽  
Gut Microbiome ◽  
Feral Horses ◽  
Microbiome Diversity ◽  
Rrna Sequencing ◽  
Domestic Horses ◽  
Species Groups ◽  
The Impact ◽  
Bacterial Groups

Abstract Background: Early development of the gut microbiome is an essential part of neonate health in animals. It is unclear whether the acquisition of gut microbes is different between domesticated animals and their wild counterparts. In this study, fecal samples from ten domestic conventionally managed (DCM) Standardbred and ten semi-feral managed (SFM) Shetland-type pony foals and dams were compared using 16S rRNA sequencing to identify differences in the development of the foal hindgut microbiome related to time and management. Results: Gut microbiome diversity of dams was lower than foals overall and within groups, and foals from both groups at Week 1 had less diverse gut microbiomes than subsequent weeks. The core microbiomes of SFM dams and foals had more taxa overall, and greater numbers of taxa within species groups when compared to DCM dams and foals. The gut microbiomes of SFM foals demonstrated enhanced diversity of key groups: Verrucomicrobia (RFP12), Ruminococcaceae, Fusobacterium spp., and Bacteroides spp., based on age and management. Lactic acid bacteria Lactobacillus spp. and other Lactobacillaceae genera were enriched only in DCM foals, specifically during their second and third week of life. Predicted microbiome functions estimated computationally suggested that SFM foals had higher mean sequence counts for taxa contributing to the digestion of lipids, simple and complex carbohydrates, and protein. DCM foal microbiomes were more similar to their dams in week five and six than were SFM foals at the same age.Conclusions: This study demonstrates the impact of management on the development of the foal gut microbiome in the first 6 weeks of life. The higher numbers of taxa within and between bacterial groups found in SFM dams and foals suggests more diversity and functional redundancy in their gut microbiomes, which could lend greater stability and resiliency to these communities. The colonization of lactic acid bacteria in the early life of DCM foals suggests enrichment in response to the availability of dams’ feed. Thus, management type is an important driver of gut microbiome establishment on horses, and we may look to semi-feral horses for guidance in defining a healthy gut microbiome for domestic horses.

scholarly journals Development of the Equine Hindgut Microbiome in Semi-feral and Domestic Conventionally-Managed Foals

2020 ◽  
Author(s):  
Meredith Tavenner ◽  
Sue M McDonnell ◽  
Amy S Biddle
Keyword(s):  
Lactic Acid ◽  
Lactic Acid Bacteria ◽  
Gut Microbiome ◽  
Feral Horses ◽  
Microbiome Diversity ◽  
Domestic Horses ◽  
Species Groups ◽  
The Impact ◽  
Bacterial Groups ◽  
Lactobacillus Spp

Abstract Background Early development of the gut microbiome is an essential part of neonate health in animals. It is unclear whether the acquisition of gut microbes is different between domesticated animals and their wild counterparts. In this study, fecal samples from ten domestic conventionally managed (DCM) Standardbred and ten semi-feral managed (SFM) Shetland-type pony foals and dams were compared using 16S rRNA sequencing to identify differences in the development of the foal hindgut microbiome related to time and management. Results Gut microbiome diversity of dams was higher than foals overall, and foals from both groups at Week 1 had less diverse gut microbiomes than subsequent weeks. The core microbiomes of SFM dams and foals had more taxa overall, and greater numbers of taxa within species groups when compared to DCM dams and foals. The gut microbiomes of SFM foals demonstrated enhanced diversity of key groups: Verrucomicrobia (RFP12), Ruminococcaceae, Fusobacterium spp., and Bacteroides spp., based on age and management. Lactic acid bacteria Lactobacillus spp. and Lactobacillaceae gen. were enriched only in DCM foals, specifically during their second and third week of life. Predicted microbiome functions estimated computationally suggested that SFM foals had higher mean sequence counts for taxa contributing to the digestion of lipids, simple and complex carbohydrates, and protein. DCM foal microbiomes were more similar to their dams in week five and six than were SFM foals at the same age. Conclusions This study demonstrates the impact of management on the development of the foal gut microbiome in the first 6 weeks of life. The higher numbers of taxa within and between bacterial groups found in SFM dams and foals suggests more diversity and functional redundancy in their gut microbiomes, which could lend greater stability and resiliency to these communities. The colonization of lactic acid bacteria in the early life of DCM foals suggests enrichment in response to the availability of dams’ feed. Thus, management type is an important driver of gut microbiome establishment on horses, and we may look to semi-feral horses for guidance in defining a healthy gut microbiome for domestic horses.

scholarly journals Altered diversity and composition of gut microbiota in Wilson's disease

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Xiangsheng Cai ◽  
Lin Deng ◽  
Xiaogui Ma ◽  
Yusheng Guo ◽  
Zhiting Feng ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Gut Microbiome ◽  
Wilson’S Disease ◽  
Wilson's Disease ◽  
Healthy Individuals ◽  
Lower Abundance ◽  
Rrna Sequencing ◽  
Healthy Control ◽  
The Impact ◽  
Bacterial Groups

AbstractWilson’s disease (WD) is an autosomal recessive inherited disorder of chronic copper toxicosis with high mortality and disability. Recent evidence suggests a correlation between dysbiosis in gut microbiome and multiple diseases such as genetic and metabolic disease. However, the impact of intestinal microbiota polymorphism in WD have not been fully elaborated and need to be explore for seeking some microbiota benefit for WD patients. In this study, the 16S rRNA sequencing was performed on fecal samples from 14 patients with WD and was compared to the results from 16 healthy individuals. The diversity and composition of the gut microbiome in the WD group were significantly lower than those in healthy individuals. The WD group presented unique richness of Gemellaceae, Pseudomonadaceae and Spirochaetaceae at family level, which were hardly detected in healthy controls. The WD group had a markedly lower abundance of Actinobacteria, Firmicutes and Verrucomicrobia, and a higher abundance of Bacteroidetes, Proteobacteria, Cyanobacteria and Fusobacteria than that in healthy individuals. The Firmicutes to Bacteroidetes ratio in the WD group was significantly lower than that of healthy control. In addition, the functional profile of the gut microbiome from WD patients showed a lower abundance of bacterial groups involved in the host immune and metabolism associated systems pathways such as transcription factors and ABC-type transporters, compared to healthy individuals. These results implied dysbiosis of gut microbiota may be influenced by the host metabolic disorders of WD, which may provide a new understanding of the pathogenesis and new possible therapeutic targets for WD.

scholarly journals Altered Diversity and Composition of Gut Microbiota in Wilson's disease

2020 ◽  
Author(s):  
Xiangsheng Cai ◽  
Lin Deng ◽  
Xiaogui Ma ◽  
Yusheng Guo ◽  
Zhiting Feng ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Gut Microbiome ◽  
Wilson’S Disease ◽  
Wilson's Disease ◽  
Healthy Individuals ◽  
Lower Abundance ◽  
Rrna Sequencing ◽  
Healthy Control ◽  
The Impact ◽  
Bacterial Groups

Abstract Background: Wilson’s disease (WD) is a rare autosomal recessive inherited disorder of chronic copper toxicosis with high mortality and disability. Recent evidence suggests a correlation between dysbiosis in the gut microbiome and metabolic disease. Therefore, the impact of intestinal microbiota polymorphism in WD need to be explore for seeking some microbiota benefit for WD patients. Methods: In this study, the 16S rRNA sequencing was performed on fecal samples from 14 patients with WD and were compared to the results from 16 healthy individuals. The diversity and composition of the gut microbiome in the WD group were significantly lower than those in healthy individuals. Results: The WD group presented unique richness of Gemellaceae , Pseudomonadaceae and Spirochaetaceae at family level in WD group, which were hardly detected in healthy controls The WD group had a markedly lower abundance of Acidobacteria , Firmicutes and Verrucomicrobia , and a higher abundance of Bacteroidet es, Proteobacteria , Cyanobacteria and Fusobacteria than that in healthy individuals. The Firmicutes to Bacteroidetes ratio in the WD group was significantly lower than that of healthy control. The functional profile of the gut microbiome from WD patients showed a lower abundance of bacterial groups involved in the pathways of transcription factors and ABC-type transporters, compared to healthy individuals. The dysbiosis of gut microbiota may be influenced by the host metabolic disorders of WD such as signaling pathway of ABC-type transporters and multiple metabolic modules. Conclusions: This study provides a new understanding of the pathogenesis of WD and new possible therapeutic targets.

scholarly journals Comparison of the Fecal Microbiota of Horses with Intestinal Disease and Their Healthy Counterparts

2021 ◽  
Vol 8 (6) ◽  
pp. 113
Author(s):  
Taemook Park ◽  
Heetae Cheong ◽  
Jungho Yoon ◽  
Ahram Kim ◽  
Youngmin Yun ◽  
...  
Keyword(s):  
Lactic Acid ◽  
Lactic Acid Bacteria ◽  
Metabolic Disorders ◽  
Bacterial Population ◽  
Fecal Microbiota ◽  
Intestinal Disease ◽  
Fecal Samples ◽  
Gut Dysbiosis ◽  
Rrna Sequencing ◽  
Small Intestinal

(1) Background: The intestinal microbiota plays an essential role in maintaining the host’s health. Dysbiosis of the equine hindgut microbiota can alter the fermentation patterns and cause metabolic disorders. (2) Methods: This study compared the fecal microbiota composition of horses with intestinal disease and their healthy counterparts living in Korea using 16S rRNA sequencing from fecal samples. A total of 52 fecal samples were collected and divided into three groups: horses with large intestinal disease (n = 20), horses with small intestinal disease (n = 8), and healthy horses (n = 24). (3) Results: Horses with intestinal diseases had fewer species and a less diverse bacterial population than healthy horses. Lactic acid bacteria, Lachnospiraceae, and Lactobacillaceae were overgrown in horses with large intestinal colic. The Firmicutes to Bacteroidetes ratio (F/B), which is a relevant marker of gut dysbiosis, was 1.94, 2.37, and 1.74 for horses with large intestinal colic, small intestinal colic, and healthy horses, respectively. (4) Conclusions: The overgrowth of two lactic acid bacteria families, Lachnospiraceae and Lactobacillaceae, led to a decrease in hindgut pH that interfered with normal fermentation, which might cause large intestinal colic. The overgrowth of Streptococcus also led to a decrease in pH in the hindgut, which suppressed the proliferation of the methanogen and reduced methanogenesis in horses with small intestinal colic.

Aroma profile and lactic acid bacteria characteristic of traditional Slovak cheese “May bryndza”

2021 ◽  
pp. 108201322110399
Author(s):  
Jana Štefániková ◽  
Július Árvay ◽  
Simona Kunová ◽  
Przemysław Łukasz Kowalczewski ◽  
Miroslava Kačániová
Keyword(s):  
Mass Spectrometry ◽  
Gas Chromatography ◽  
Lactic Acid ◽  
Lactic Acid Bacteria ◽  
Butanoic Acid ◽  
Aroma Profile ◽  
Volatile Organic ◽  
Ewe's Milk ◽  
The Impact

This paper describes the results of the characterization of a traditional Slovak cheese called “May bryndza” with regard to the profiles of volatile organic compounds and lactic acid bacteria. Samples of “May bryndza“ cheese produced solely from unpasteurized ewe's milk were collected from 4 different Slovak farms, and samples of the cheese produced from a mixture of 2 types of milk (raw ewe's and pasteurized cow's milk) were collected from 3 different Slovak industrial dairies. There were 15 compounds detected and identified by the electronic nose. The impact of the kind of milk and the kind of dairy on the aroma profile of the product was not confirmed by PCA. The compounds with the highest relative contents in samples were acetoin (2.59%–24.55%), acetic acid (6.69%–13.39%), methoxy-phenyl-oxime (4.49%–8.52%), butanoic acid (1.89%–5.67%), and 2,3-butanediol (0.98%–4.08%), which were determined with gas chromatography. A total of 1533 isolates of LAB were obtained from the “May bryndza” cheese samples. Four families, five genera, and 19 species were identified with mass spectrometry, and isolated bacteria, both from the farm and industry dairies were the most frequently found to belong to Lactococcus lactis subsp. lactis.

scholarly journals Behavior of Listeria innocua during the manufacturing and pit-ripening of Formaggio di Fossa di Sogliano PDO cheese

2020 ◽  
Vol 9 (2) ◽  
Author(s):  
Federica Giacometti ◽  
Paolo Daminelli ◽  
Laura Fiorentini ◽  
Elena Cosciani-Cunico ◽  
Paola Monastero ◽  
...  
Keyword(s):  
Lactic Acid ◽  
Lactic Acid Bacteria ◽  
Risk Mitigation ◽  
Scientific Evidence ◽  
Challenge Test ◽  
Mitigation Strategy ◽  
Listeria Innocua ◽  
Ripening Process ◽  
Protected Designation Of Origin ◽  
The Impact

Formaggio di Fossa di Sogliano is a traditional Italian Protected Designation of Origin (PDO) cheese ripened for a minimum of 5 months, with the feature of a ripening of at least 80 to at most 100 days in pits, digged into tuffaceous rocks according to medieval tradition of Italy. In this study, a challenge test using Listeria innocua as a surrogate of Listeria monocytogenes was performed, with the aim of increasing knowledge concerning the impact of the Fossa cheese process, and especially of the traditional ripening process of this PDO, on the behaviour of L. monocytogenes. Pasteurized milk was experimentally inoculated with 4.5 log CFU/mL cocktail by three L. innocua strains, and L. innocua and Mesophilic Lactic Acid Bacteria (LAB) counts as well as the evolution of temperatures, pH and aw values were monitored throughout the manufacturing and ripening processes. Throughout the ripening in maturation room a constant temperature of 8°C was observed reaching a temperature between 10 and 15.5°C during ripening into pit. In the final products data for LAB concentration, pH and aw values were roughly in accordance with literature, even if some differences were, probably due to variability of artisanal cheese productions. The numbers of L. innocua showed a slight decrease but remained stable until the end of ripening in maturation room, whereas a significant reduction of the microorganism was observed in the final product, at the end of the ripening into the pit. The findings give scientific evidence that the process of this PDO prevented the L. innocua growth, allowing us to speculate a similar behaviour of L. monocytogenes. Based on this study, the recommendation to extend as much as possible the ripening into pit (from 80 to 100 days) was provided to food business operators as a risk mitigation strategy to be implemented.

scholarly journals Inulin Fermentation by Lactobacilli and Bifidobacteria from Dairy Calves

2020 ◽  
Vol 87 (1) ◽  
Author(s):  
Yuanting Zhu ◽  
Jinxin Liu ◽  
Julian M. Lopez ◽  
David A. Mills
Keyword(s):  
Lactic Acid ◽  
Lactic Acid Bacteria ◽  
Gut Microbiome ◽  
Animal Health ◽  
Dairy Calves ◽  
Milk Replacer ◽  
Comparative Genomic ◽  
Bacterial Strains ◽  
Content Type ◽  
Long Chain

ABSTRACT Prebiotics are increasingly examined for their ability to modulate the neonate gut microbiota of livestock, and products such as inulin are commonly added to milk replacer used in calving. However, the ability of specific members of the bovine neonate microbiota to respond to inulin remains to be determined, particularly among indigenous lactobacilli and bifidobacteria, beneficial genera commonly enriched by inulin. Screening of Bifidobacterium and Lactobacillus isolates obtained from fresh feces of dairy calves revealed that lactobacilli had a higher prevalence of inulin fermentation capacity (58%) than bifidobacteria (17%). Several Ligilactobacillus agilis (synonym Lactobacillus agilis) isolates exhibited vigorous growth on, and complete degradation of, inulin; however, the phenotype was strain specific. The most vigorous inulin-fermenting strain, L. agilis YZ050, readily degraded long-chain inulin not consumed by bifidobacterial isolates. Comparative genomic analysis of both L. agilis fermenter and nonfermenter strains indicated that strain YZ050 encodes an inulinase homolog, previously linked to extracellular degradation of long-chain inulin in Lacticaseibacillus paracasei, that was strongly induced during growth on inulin. Inulin catabolism by YZ050 also generates extracellular fructose, which can cross-feed other non-inulin-fermenting lactic acid bacteria isolated from the same bovine feces. The presence of specific inulin-responsive bacterial strains within calf gut microbiome provides a mechanistic rationale for enrichment of specific lactobacilli and creates a foundation for future synbiotic applications in dairy calves aimed at improving health in early life. IMPORTANCE The gut microbiome plays an important role in animal health and is increasingly recognized as a target for diet-based manipulation. Inulin is a common prebiotic routinely added to animal feeds; however, the mechanism of inulin consumption by specific beneficial taxa in livestock is ill defined. In this study, we examined Lactobacillus and Bifidobacterium isolates from calves fed inulin-containing milk replacer and characterized specific strains that robustly consume long-chain inulin. In particular, novel Ligilactobacillus agilis strain YZ050 consumed inulin via an extracellular fructosidase, resulting in complete consumption of all long-chain inulin. Inulin catabolism resulted in temporal release of extracellular fructose, which can promote growth of other non-inulin-consuming strains of lactic acid bacteria. This work provides the mechanistic insight needed to purposely modulate the calf gut microbiome via the establishment of networks of beneficial microbes linked to specific prebiotics.

scholarly journals Large-scale genome-wide analysis links lactic acid bacteria from food with the gut microbiome

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Edoardo Pasolli ◽  
Francesca De Filippis ◽  
Italia E. Mauriello ◽  
Fabio Cumbo ◽  
Aaron M. Walsh ◽  
...  
Keyword(s):  
Lactic Acid ◽  
Lactic Acid Bacteria ◽  
Gut Microbiome ◽  
Large Scale ◽  
Streptococcus Thermophilus ◽  
Fermented Food ◽  
Fermented Foods ◽  
Genome Wide Analysis ◽  
Genome Wide ◽  
Stool Samples

Abstract Lactic acid bacteria (LAB) are fundamental in the production of fermented foods and several strains are regarded as probiotics. Large quantities of live LAB are consumed within fermented foods, but it is not yet known to what extent the LAB we ingest become members of the gut microbiome. By analysis of 9445 metagenomes from human samples, we demonstrate that the prevalence and abundance of LAB species in stool samples is generally low and linked to age, lifestyle, and geography, with Streptococcus thermophilus and Lactococcus lactis being most prevalent. Moreover, we identify genome-based differences between food and gut microbes by considering 666 metagenome-assembled genomes (MAGs) newly reconstructed from fermented food microbiomes along with 154,723 human MAGs and 193,078 reference genomes. Our large-scale genome-wide analysis demonstrates that closely related LAB strains occur in both food and gut environments and provides unprecedented evidence that fermented foods can be indeed regarded as a possible source of LAB for the gut microbiome.

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