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A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Gut Microbiota".

Deadline for manuscript submissions: closed (30 September 2021) | Viewed by 36992

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Dr. Benoit St Pierre

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Department of Animal Science, South Dakota State University, Animal Science Complex, Box 2170, Brookings, SD 57007, USA
Interests: gut microbiota; microbial ecology; bioinformatics; food animals; metagenomics
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Dear Colleagues,

Ruminants represent a highly successful biological group that has not only thrived across a wide range of habitats but also played a central role throughout human history. Even to this day, the ability of domesticated ruminants to transform inedible plant biomass into products that can be consumed or utilized by humans is essential in meeting the demands of a rapidly growing and urbanizing global population.

Ruminants are able to metabolize cellulosic biomass because of the metabolic activities of symbiotic microbial communities that reside in the rumen compartment of their gastrointestinal tract. Elucidating the complexities of ruminal microbial communities remains a challenging subject for basic and applied scientists. As Guest Editor, I am encouraging submissions on this topic. These can include composition and/or functional dynamics of ruminal bacterial, archaeal, protozoal, and/or fungal communities from domesticated or non-domesticated ruminant hosts in response to dietary treatments or other conditions, as well as host–microbiome interactions, and interactions amongst microbial species/groups or microbial ecology of the rumen environment. Reviews and research articles, including short communications, on these topics are welcome.

Dr. Benoit St Pierre
Guest Editor

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Published Papers (11 papers)

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Editorial

Jump to: Research

3 pages, 188 KiB

Open AccessEditorial

Special Issue “Rumen Microbial Communities”: Editorial

by Benoit St-Pierre

Microorganisms 2023, 11(4), 919; https://doi.org/10.3390/microorganisms11040919 - 1 Apr 2023

Viewed by 1082

Abstract

Ruminants represent a highly successful group of herbivores that have not only evolved to thrive across a wide range of habitats, but have also played a central role throughout human history [...] Full article

(This article belongs to the Special Issue Rumen Microbial Communities)

Research

Jump to: Editorial

14 pages, 2371 KiB

Open AccessArticle

The Temporal Dynamics of Rumen Microbiota in Early Weaned Lambs

by Shiqin Wang, Jianmin Chai, Guohong Zhao, Naifeng Zhang, Kai Cui, Yanliang Bi, Tao Ma, Yan Tu and Qiyu Diao

Microorganisms 2022, 10(1), 144; https://doi.org/10.3390/microorganisms10010144 - 11 Jan 2022

Cited by 11 | Viewed by 2798

Abstract

Weaning affects the development of ruminal bacteria in lambs during early life. However, the temporal dynamics of rumen microbiota in early weaned lambs is unknown compared to conventionally weaned lambs. In this study, one group was reared with their dams (control, CON) and conventionally weaned at 49 days (d), while the other lambs were weaned at 21 d (early weaning, EW) using starter. Rumen microbial samples collected at 26, 35, and 63 d were used for next-generation sequencing. Here, we found that the abundance and diversity of rumen microbiota in EW were significantly lower at 26 and 35 d than the CON. Linear discriminant analysis Effect Size (LEfSe) analysis was performed to identify the signature microbiota for EW at these three ages. At 26 d, Prevotella 7, Syntrophococcus, Sharpea, Dialister, Pseudoscardovia, and Megasphaera in the rumen of the EW group had greater relative abundances. At 35 d, the Lachnospiraceae_NK3A20_group was enriched in CON. On 63 d, Erysipelotrichaceae_UCG-002 was abundant in EW. Syntrophococcus and Megaspheaera in EW lambs were abundant at 26 and 35 d, but kept similar to CON at 63 d. The relative abundance of Erysipelotrichaceae_UCG-002 at all-time points was consistently higher in the EW group. In conclusion, early weaning led to a significant decrease in rumen microbiota richness and diversity in the short term. The changes in rumen microbiota are associated with the persistence of weaning stress. The temporal dynamics of relative abundances of Syntrophococcus, Megasphaera, and Ruminococcaceae_UCG-014 reflect the weaning stress over a short period and rumen recovery after early weaning. Full article

(This article belongs to the Special Issue Rumen Microbial Communities)

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19 pages, 2974 KiB

Open AccessArticle

Characterizing the Alteration in Rumen Microbiome and Carbohydrate-Active Enzymes Profile with Forage of Muskoxen Rumen through Comparative Metatranscriptomics

by Xiaofeng Wu, Chijioke O. Elekwachi, Shiping Bai, Yuheng Luo, Keying Zhang and Robert J. Forster

Microorganisms 2022, 10(1), 71; https://doi.org/10.3390/microorganisms10010071 - 30 Dec 2021

Cited by 6 | Viewed by 2717

Abstract

Muskox (Ovibos moschatus), as the biggest herbivore in the High Arctic, has been enduring the austere arctic nutritional conditions and has evolved to ingest and digest scarce and high lignified forages to support the growth and reproduce, implying probably harbor a distinct microbial reservoir for the deconstruction of plant biomass. Therefore, metagenomics approach was applied to characterize the rumen microbial community and understand the alteration in rumen microbiome of muskoxen fed either triticale straw or brome hay. The difference in the structure of microbial communities including bacteria, archaea, fungi, and protozoa between the two forages was observed at the taxonomic level of genus. Further, although the highly abundant phylotypes in muskoxen rumen fed either triticale straw or brome hay were almost the same, the selective enrichment different phylotypes for fiber degrading, soluble substrates fermenting, electron and hydrogen scavenging through methanogenesis, acetogenesis, propionogenesis, and sulfur-reducing was also noticed. Specifically, triticale straw with higher content of fiber, cellulose selectively enriched more lignocellulolytic taxa and electron transferring taxa, while brome hay with higher nitrogen content selectively enriched more families and genera for degradable substrates-digesting. Intriguingly, the carbohydrate-active enzyme profile suggested an over representation and diversity of putative glycoside hydrolases (GHs) in the animals fed on triticale straw. The majority of the cellulases belonged to fiver GH families (i.e., GH5, GH6, GH9, GH45, and GH48) and were primarily synthesized by Ruminococcus, Piromyces, Neocallimastix, and Fibrobacter. Abundance of major genes coding for hemicellulose digestion was higher than cellulose mainly including GH8, GH10, GH16, GH26, and GH30, and these enzymes were produced by members of the genera Fibrobacter, Ruminococcus, and Clostridium. Oligosaccharides were mainly of the GH1, GH2, GH3, and GH31 types and were associated with the genera Prevotella and Piromyces. Our results strengthen metatranscriptomic evidence in support of the understanding of the microbial community and plant polysaccharide response to changes in the feed type and host animal. The study also establishes these specific microbial consortia procured from triticale straw group can be used further for efficient plant biomass hydrolysis. Full article

(This article belongs to the Special Issue Rumen Microbial Communities)

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28 pages, 7448 KiB

Open AccessArticle

The Nasopharyngeal, Ruminal, and Vaginal Microbiota and the Core Taxa Shared across These Microbiomes in Virgin Yearling Heifers Exposed to Divergent In Utero Nutrition during Their First Trimester of Gestation and in Pregnant Beef Heifers in Response to Mineral Supplementation

by Samat Amat, Devin B. Holman, Kaycie Schmidt, Ana Clara B. Menezes, Friederike Baumgaertner, Thomas Winders, James D. Kirsch, Tingting Liu, Timothy D. Schwinghamer, Kevin K. Sedivec and Carl R. Dahlen

Microorganisms 2021, 9(10), 2011; https://doi.org/10.3390/microorganisms9102011 - 23 Sep 2021

Cited by 24 | Viewed by 3596

Abstract

In the present study, we evaluated whether the nasopharyngeal, ruminal, and vaginal microbiota would diverge (1) in virgin yearling beef heifers (9 months old) due to the maternal restricted gain during the first trimester of gestation; and (2) in pregnant beef heifers in response to the vitamin and mineral (VTM) supplementation during the first 6 months of pregnancy. As a secondary objective, using the microbiota data obtained from these two cohorts of beef heifers managed at the same location and sampled at the same time, we performed a holistic assessment of the microbial ecology residing within the respiratory, gastrointestinal, and reproductive tract of cattle. Our 16S rRNA gene sequencing results revealed that both α and β-diversity of the nasopharyngeal, ruminal and vaginal microbiota did not differ between virgin heifers raised from dams exposed to either a low gain (targeted average daily gain of 0.28 kg/d, n = 22) or a moderate gain treatment (0.79 kg/d, n = 23) during the first 84 days of gestation. Only in the vaginal microbiota were there relatively abundant genera that were affected by maternal rate of gain during early gestation. Whilst there was no significant difference in community structure and diversity in any of the three microbiota between pregnant heifers received no VTM (n = 15) and VTM supplemented (n = 17) diets, the VTM supplementation resulted in subtle compositional alterations in the nasopharyngeal and ruminal microbiota. Although the nasopharyngeal, ruminal, and vaginal microbiota were clearly distinct, a total of 41 OTUs, including methanogenic archaea, were identified as core taxa shared across the respiratory, gastrointestinal, and reproductive tracts of both virgin and pregnant heifers. Full article

(This article belongs to the Special Issue Rumen Microbial Communities)

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11 pages, 4630 KiB

Open AccessArticle

Geographical Relationships between Long-Tailed Goral (Naemorhedus caudatus) Populations Based on Gut Microbiome Analysis

by Chang Eon Park, Bum-Joon Cho, Min-Ji Kim, Hee Cheon Park and Jae-Ho Shin

Microorganisms 2021, 9(9), 2002; https://doi.org/10.3390/microorganisms9092002 - 21 Sep 2021

Cited by 4 | Viewed by 4351

Abstract

The long-tailed goral (Naemorhedus caudatus) is an endangered species found in the mountains of eastern and northern Asia. Its populations have declined for various reasons, and this species has been designated as legally protected in South Korea. Although various ecological studies have been conducted on long-tailed gorals, none have investigated the gut microbiome until now. In the present study, we compared the diversity and composition of the gut microbiome of seven populations of Korean long-tailed gorals. By analyzing the gut microbiome composition for each regional population, it was found that four phyla—Firmicutes, Actinobacteriota, Bacteroidota, and Proteobacteria—were the most dominant in all regions on average. The alpha diversity of the gut microbiome of the goral population in the northern regions was high, while that in the southern regions was low. Through the analysis of beta diversity, the seven long-tailed goral populations have been divided into three groups: the Seoraksan population, the Samcheock population, and the Wangpicheon population. It was possible to confirm the regional migration of the animals using the gut microbiome based on the site-relational network analysis. It was found that the most stable population of long-tailed gorals in Korea was the Seoraksan population, and the closely related groups were the Samcheok and Wangpicheon populations, respectively. Wangpicheon appeared to be a major point of dispersal in the migration route of Korean long-tailed gorals. Full article

(This article belongs to the Special Issue Rumen Microbial Communities)

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14 pages, 1821 KiB

Open AccessArticle

Effects of Age, Diet CP, NDF, EE, and Starch on the Rumen Bacteria Community and Function in Dairy Cattle

by Yangyi Hao, Yue Gong, Shuai Huang, Shoukun Ji, Wei Wang, Yajing Wang, Hongjian Yang, Zhijun Cao and Shengli Li

Microorganisms 2021, 9(8), 1788; https://doi.org/10.3390/microorganisms9081788 - 23 Aug 2021

Cited by 14 | Viewed by 3547

Abstract

To understand the effects of diet and age on the rumen bacterial community and function, forty-eight dairy cattle at 1.5 (M1.5), 6 (M6), 9 (M9), 18 (M18), 23 (M23), and 27 (M27) months old were selected. Rumen fermentation profile, enzyme activity, and bacteria community in rumen fluid were measured. The acetate to propionate ratio (A/P) at M9, M18, and M23 was higher than other ages, and M6 was the lowest (p < 0.05). The total volatile fatty acid (TVFA) at M23 and M27 was higher than at other ages (p < 0.05). The urease at M18 was lower than at M1.5, M6, and M9, and the xylanase at M18 was higher than at M1.5, M23, and M27 (p < 0.05). Thirty-three bacteria were identified as biomarkers of the different groups based on the linear discriminant analysis (LDA) when the LDA score >4. The variation partitioning approach analysis showed that the age and diet had a 7.98 and 32.49% contribution to the rumen bacteria community variation, respectively. The richness of Succinivibrionaceae_UCG-002 and Fibrobacter were positive correlated with age (r > 0.60, p < 0.01) and positively correlated with TVFA and acetate (r > 0.50, p < 0.01). The Lachnospiraceae_AC2044_group, Pseudobutyrivibrio, and Saccharofermentans has a positive correlation (r > 0.80, p < 0.05) with diet fiber and a negative correlation (r < −0.80, p < 0.05) with diet protein and starch, which were also positively correlated with the acetate and A/P (r > 0.50, p < 0.01). The genera of Lachnospiraceae_AC2044_group, Pseudobutyrivibrio, and Saccharofermentans could be worked as the target bacteria to modulate the rumen fermentation by diet; meanwhile, the high age correlated bacteria such as Succinivibrionaceae_UCG-002 and Fibrobacter also should be considered when shaping the rumen function. Full article

(This article belongs to the Special Issue Rumen Microbial Communities)

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23 pages, 8578 KiB

Open AccessArticle

Changes in the Rumen Bacteriome Structure and Enzymatic Activities of Goats in Response to Dietary Supplementation with Schizochytrium spp.

by Alexandros Mavrommatis, Dimitrios Skliros, Emmanouil Flemetakis and Eleni Tsiplakou

Microorganisms 2021, 9(7), 1528; https://doi.org/10.3390/microorganisms9071528 - 17 Jul 2021

Cited by 15 | Viewed by 4142

Abstract

With the aim to produce functional dairy products enriched with polyunsaturated fatty acids (PUFA) by using feed supplements, radical changes could occur in the rumen microbiome. This work investigated the alterations of the rumen bacteriome of goats fed with PUFA-rich marine microalgae Schizochytrium spp. For the trial, twenty-four goats were divided into four homogenous clusters (six goats/treatment) according to their fat-corrected (4%) milk yield, body weight, and age; they were individually fed with alfalfa hay and a concentrate (F/C = 50/50). The concentrate of the control group (CON) contained no microalgae, while those of the treated groups were supplemented daily with 20 (ALG20), 40 (ALG40), and 60 g (ALG60) of Schizochytrium spp./goat. Rumen fluid samples were collected using a stomach tube during the 20th and 40th days of the experiment. The microbiome analysis using a 16S rRNA sequencing platform revealed that Firmicutes were decreased in microalgae-fed goats, while Bacteroidetes showed a tendency to increase in the ALG40 group due to the enhancement of Prevotellaceae. Cellulolytic bacteria, namely Treponema bryantii, Ruminococcus gauvreauii, R. albus, and R. flavefaciens, were decreased in the ALG40 group, resulting in an overall decrease of cellulase activity. In contrast, the amylolytic potential was significantly enhanced due to an upsurge in Ruminobacter amylophilus, Succinivibrio dextrinosolvens, and Fretibacterium fastidiosum populations. In conclusion, supplementing goats’ diets with 20 g Schizochytrium spp. could be considered a sustainable and efficient nutritional strategy to modulate rumen microbiome towards the development of dairy products enriched with bioactive compounds, while higher levels induced substantial shifts in determinant microbes’ populations. Full article

(This article belongs to the Special Issue Rumen Microbial Communities)

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14 pages, 2323 KiB

Open AccessArticle

Long-Term Effects of Dietary Supplementation with Olive Oil and Hydrogenated Vegetable Oil on the Rumen Microbiome of Dairy Cows

by Nathaly Cancino-Padilla, Natalia Catalán, Karen Siu-Ting, Christopher J. Creevey, Sharon A. Huws, Jaime Romero and Einar Vargas-Bello-Pérez

Microorganisms 2021, 9(6), 1121; https://doi.org/10.3390/microorganisms9061121 - 22 May 2021

Cited by 10 | Viewed by 3287

Abstract

Dietary lipids increase energy density in dairy cow diets and in some cases can increase beneficial fatty acids (FA) in milk and dairy products. However, the degree of FA saturation may affect the rumen microbiome. The objective of this study was to determine the long-term effects of feeding saturated (hydrogenated vegetable oil; HVO) or unsaturated (olive oil; OO) fatty acid (FA) sources on the rumen microbiome of dairy cows. For 63 days, 15 mid-lactating cows were fed with either a basal diet (no fat supplement), or the basal diet supplemented with 3% dry matter (DM), either HVO or OO. Rumen contents were collected on days 21, 42 and 63 for 16S rRNA gene sequencing using the Illumina MiSeq platform. The results reveal dominance of the phyla Firmicutes (71.5%) and Bacteroidetes (26.2%), and their respective prevalent genera Succiniclasticum (19.4%) and Prevotella (16.6%). Succiniclasticum increased with both treatments at all time points. Prevotella was reduced on day 42 in both diets. Bacterial diversity alpha or beta were not affected by diets. Predicted bacterial functions by CowPI showed changes in energy and protein metabolism. Overall, 3% DM of lipid supplementation over 63 days can be used in dairy cow diets without major impacts on global bacterial community structure. Full article

(This article belongs to the Special Issue Rumen Microbial Communities)

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14 pages, 3144 KiB

Open AccessArticle

Metagenomic Insight: Dietary Thiamine Supplementation Promoted the Growth of Carbohydrate-Associated Microorganisms and Enzymes in the Rumen of Saanen Goats Fed High-Concentrate Diets

by Ying Zhang, Chao Wang, Along Peng, Hao Zhang and Hongrong Wang

Microorganisms 2021, 9(3), 632; https://doi.org/10.3390/microorganisms9030632 - 18 Mar 2021

Cited by 8 | Viewed by 2526

Abstract

Subacute ruminal acidosis (SARA) is often caused by feeding a high-concentrate diet in intensive ruminant production. Although previous studies have shown that dietary thiamine supplementation can effectively increase rumen pH and modify rumen fermentation, the effect of thiamine supplementation on rumen carbohydrate-related microorganisms and enzymes in goats under SARA conditions remain unclear. Therefore, the objective of the present study was to investigate the effects of dietary thiamine supplementation on carbohydrate-associated microorganisms and enzymes in the rumen of Saanen goats fed high-concentrate diets. Nine healthy mid-lactating Saanen goats in parity 1 or 2 were randomly assigned into three treatments: A control diet (CON; concentrate:forage (30:70)), a high-concentrate diet (HC; concentrate:forage (70:30)), and a high-concentrate diet with 200 mg of thiamine/kg of DMI (HCT; concentrate:forage (70:30)). Compared with the HC group, dietary thiamine supplementation improved ruminal microbes associated with fiber, including Prevotella, Fibrobacter, Neocallimastix, and Piromyces (p < 0.05). In addition, an increase in the relative abundance of enzymes involved in both fiber degradation and starch degradation, such as CBM16, GH3, and GH97, was observed in the HCT treatment. (p < 0.05). Thus, thiamine supplementation can improve carbohydrate metabolism by increasing the abundance of the microorganisms and enzymes involved in carbohydrate degradation. In conclusion, this study revealed the relationship between ruminal microbiota and enzymes, and these findings contributed to solving the problems arising from the high-concentrate feeding in ruminant production and to providing a new perspective on ruminant health. Full article

(This article belongs to the Special Issue Rumen Microbial Communities)

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22 pages, 9674 KiB

Open AccessArticle

Unveiling the Bovine Epimural Microbiota Composition and Putative Function

by Cátia Pacífico, Renée Maxine Petri, Sara Ricci, Elsayed Mickdam, Stefanie Urimare Wetzels, Viktoria Neubauer and Qendrim Zebeli

Microorganisms 2021, 9(2), 342; https://doi.org/10.3390/microorganisms9020342 - 9 Feb 2021

Cited by 27 | Viewed by 4307

Abstract

Numerous studies have used the 16S rRNA gene target in an attempt to characterize the structure and composition of the epimural microbiota in cattle. However, comparisons between studies are challenging, as the results show large variations associated with experimental protocols and bioinformatics methodologies. Here, we present a meta-analysis of the rumen epimural microbiota from 11 publicly available amplicon studies to assess key technical and biological sources of variation between experiments. Using the QIIME2 pipeline, 332 rumen epithelial microbiota samples were analyzed to investigate community structure, composition, and functional potential. Despite having a significant impact on microbial abundance, country of origin, farm, hypervariable region, primer set, animal variability, and biopsy location did not obscure the identification of a core microbiota. The bacterial genera Campylobacter, Christensenellaceae R-7 group, Defluviitaleaceae UCG-011, Lachnospiraceae UCG-010, Ruminococcaceae NK4A214 group, Ruminococcaceae UCG-010, Ruminococcaceae UCG-014, Succiniclasticum, Desulfobulbus, and Comamonas spp. were found in nearly all epithelium samples (>90%). Predictive analysis (PICRUSt) was used to assess the potential functions of the epithelial microbiota. Regularized canonical correlation analysis identified several pathways associated with the biosynthesis of precursor metabolites in Campylobacter, Comamonas, Desulfobulbus, and Ruminococcaceae NK4A214, highlighting key metabolic functions of these microbes within the epithelium. Full article

(This article belongs to the Special Issue Rumen Microbial Communities)

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13 pages, 1111 KiB

Open AccessArticle

Identification of a Candidate Starch Utilizing Strain of Prevotella albensis from Bovine Rumen

by Venkata Vinay Kumar Bandarupalli and Benoit St-Pierre

Microorganisms 2020, 8(12), 2005; https://doi.org/10.3390/microorganisms8122005 - 16 Dec 2020

Cited by 12 | Viewed by 2876

Abstract

The inclusion of starch-rich feedstuffs, a common practice in intensive ruminant livestock production systems, can result in ruminal acidosis, a condition that can severely impact animal performance and health. One of the main causes of acidosis is the rapid accumulation of ruminal short chain fatty acids (SCFAs) resulting from the microbial digestion of starch. A greater understanding of ruminal bacterial amylolytic activities is therefore critical to improving mitigation of acidosis. To this end, our manuscript reports the identification of a candidate starch utilizer (OTU SD_Bt-00010) using batch culturing of bovine rumen fluid supplemented with starch. Based on 16S rRNA gene sequencing and metagenomics analysis, SD_Bt-00010 is predicted to be a currently uncharacterized strain of Prevotella albensis. Annotation of de novo assembled contigs from metagenomic data not only identified sequences encoding for α-amylase enzymes, but also revealed the potential to metabolize xylan as an alternative substrate. Metagenomics also predicted that SCFA end products for SD_Bt-00010 would be acetate and formate, and further suggested that this candidate strain may be a lactate utilizer. Together, these results indicate that SD_Bt-00010 is an amylolytic symbiont with beneficial attributes for its ruminant host. Full article

(This article belongs to the Special Issue Rumen Microbial Communities)

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