Ruminants
Bovine cattle and other ruminants have a different digestive system compared to other mammals, and therefore the ruminant gut microbiota is very interesting for us in Microbial Ecology. Moreover, some members of the ruminant gut microbiota produce methane, a greenhouse gas. Here you can find some comments, papers and discussions that you may find useful in your career.
Last update: July 14, 2023
Papers
1944
"The significance of the bacteria and the protozoa of the rumen of the bovine" by E. G. Hastings.
When referring to symbiosis in the rumen microbiota, the author says:
"The spatial arrangements are never included in the specifications but, by usage, the term is commonly restricted to those forms living in such intimacy that, so far as space is concerned, the associated forms comprise a unit, a family."
"This population has arisen from the material ingested by the animal and to think that this microbial population has no role in the economy of the animal is possible only for one who has had no training in microbiology".
"Studies on cellulose fermentation: I. The culture and physiology of an anaerobic cellulose-digesting bacterium" by Hungate.
1951
"Choline Deficiency in the Calf" by Johnson et al.
1953
"A quantitative study of rumen synthesis in the bovine and natural and purified diets. II. Riboflavin, pantothenic acid and niacin" by Agrawala et al.
This paper is very interesting.
"The ingesta obtained from 7 trials with rumen fistulated calves were analyzed microbiologically to determine the capacity of rumen microorganisms to synthesize riboflavin, pantothenic acid and niacin from the medium components of a purified ration which contained urea as the only essential source of nitrogen. Quantitative evidence was obtained to indicate that the microorganisms were able to synthesize as much riboflavin and niacin, but only 50% as much pantothenic acid, within 6 hours after feeding as was found in the rumen of a calf maintained on a natural ration."
The average of 7 trials showed that the calves on the purified ration synthesized 20, 31 and 154 mg of riboflavin, pantothenic acid and niacin, respectively, within 6 hours after feeding. The increased amounts of these B vitamins found in the rumen of the calf on the natural ration were approximately equivalent to the amounts ingested in the feed.
"The rates of absorption of acetic, propionic and n-butyric acids" by Pfander and Phillipson.
1954
"The magnitude of the microbial fermentation in the bovine rumen" by Carroll and Hungate.
Indeed, one of the most interesting papers on ruminal microbial fermentation. In here, the authors wrote:
"The agreement between the estimates of the relative importance of the rumen fermentation for the hay and grain experiments is fairly good and it may be tentatively concluded that the volatile acids produced in the rumen account for about 70 per cent of the total energy requirement. The mechanisms by which the remaining requirement is met presumably include 1) digestion of protein and other materials in the abomasum, 2) fermentation in the large intestine, and 3) formation in the rumen of additional products such as lactic and succinic acids."
This is actually not that surprinsing, in here you can find another reference that says the following about the human gut microbiome:
"We estimate that microbial metabolism in the human gut, for example, produces 61 kcal/h, which corresponds to approximately 70% of the total heat production of an average person at rest."
1960
"Symposium: selected topics in microbial ecology. I. Microbial ecology of the rumen" by Hungate.
1961
"Butyrate metabolism in the lactating cow" by Black et al.
In this paper, the authors mentioned that Carroll and Hungate (1954, see above) have estimated that the acetate, propionate, and butyrate produced in the rumen provide approximately 70% of the total energy requirement in the bovine".
1963
"Succinic Acid Turnover and Propionate Production in the Bovine Rumen" by Blackburn and Hungate.
1964
"Acetate metabolism in the ruminant" by Sabine and Johnson.
1965
"Normal intestinal flora of cattle fed high-roughage rations" by Maki and Picard.
The authors said that the direct counts of intestinal contents indicated that 1 to 10% of the bacteria present were recovered.
1966
"Medium without rumen fluid for nonselective enumeration and isolation of rumen bacteria" by Caldwell and Byrant.
1967
"Inhibition of rumen methanogenesis by methane analogues" by Dubos.
1974
"Yeasts and moulds in the bovine rumen" by A. Lund.
The author did not find Saccharomyces.
1975
"The rumen microbial ecosystem" by Hungate.
1976
"Role of choline in the nutrition of the rumen protozoa Entodinium caudatum" by Broad and Dawson.
"Factors influencing rumen fermentation: effect of hydrogen on formation of propionate" by Schulman and Valentino.
1978
"Bacterial flora in the digestive tract of cattle. I. Comparison of nonselective culture medium and changes in fecal bacterial flora with age" by Watase and Takenouchi.
"Ruminococcus flavefaciens cell coat and adhesion to cotton cellulose and to cell walls in leaves of perennial ryegrass (Lolium perenne)" by Latham et al.
1979
"Rumen anaerobic fungi of cattle and sheep" by Bauchop.
1983
"Association of methanogenic bacteria with rumen protozoa" by Krumholz et al.
1986
"Ruminal evacuation's effect on microbial activity and ruminal function" by Towne et al., including TG Nagaraja.
I personally have never seen these (exciting) types of studies.
1988
"Influence of major minerals on rumen microbiota" by Durand and Komisarczu.
1990
"Genetic diversity in Selenmonas ruminantium isolated from the rumen" by Flint and Bisset.
1991
In a study of the effect of a Saccharomyces cerevisiaea culture on lactate utilization by the ruminal bacterium Selenomonas ruminantium, Nisbet and a Martin mentioned that "Selenomonas ruminantium is a common gram-negative ruminal bacterium that can account for up to 51% of the total viable bacterial counts within the rumen" citing an earlier paper published by Caldwell and Bryant from 1966 (link to PDF). Although this statement is not neccessarily wrong, what is wrong is to say that S. ruminantium is an abundant member of the rumen microbiota, at least based on the study mentioned below in 2013.
1992
"A net carbohydrate and protein system for evaluating cattle diets. II. Ruminal fermentation" by Russell et al.
1993
"Isolation and characterization of Selenomonas ruminantium strains capable of 2-Deoxyribose utilization" by Mark A. Rasmussen.
I honestly never thought about nucleic acids being a "substrate" for rumen fermentation:
"Nucleic acids are a significant substrate for rumen fermentation, given their ubiquitous presence in plant material,microbial biomass, and sloughed ruminal epithelium"
1994
"Establishment of hydrogen-utilizing bacteria in the rumen of the newborn lamb" by Morvan et al.
"Ruminal microbiology, biotechnology, and ruminant nutrition: progress and problems" by Wallace.
1995
"Survey of urease activity in ruminal bacteria isolated from domestic and wild ruminants" by Lauková and Koniarová.
"Succiniclasticum ruminis gen. nov., sp. nov., a ruminal bacterium converting succinate to propionate as the sole energy-yielding mechanism" by van Gylswyk.
1996
"Genetic transfer of lactate-utilizing ability in the rumen bacterium Selenomonas ruminantium" by Gilmour et al.
"Why Do Many Ruminal Bacteria Die and Lyse So Quickly?" by Wells and Russell.
"Effects of a strain of Saccharomyces cerevisiae (Levucell SC1), a microbial additive for ruminants, on lactate metabolism in vitro" by Chaucheyras et al.
S. cerevisiae is a very interesting microorganism. In this website, it says something particularly intriguing:
Levucell® SC, Saccharomyces cerevisiae CNCM I-1077, es el único probiótico de levadura seca de origen natural, activa y específica para el rumen, que ha sido seleccionado para ayudar a optimizar la función ruminal de los bovinos. Esta cepa de levadura – CNCM I-1077 – fue seleccionada entre miles de cepas por ser útil para potenciar el rendimiento del ganado.
1998
"Large plasmids in ruminal strains of Selenomonas ruminantium" by Fliegerová et al.
Interestingly, this paper also makes reference to the paper published by Caldwell and Bryant in 1966 where it says that S. ruminantium is an abundant member of the rumen bacterial microbiota.
"The Importance of pH in the Regulation of Ruminal Acetate to Propionate Ratio and Methane Production In Vitro" by Russell.
2000
"Relative contributions of bacteria, protozoa, and fungi to in vitro degradation of orchard grass cell walls and their interactions" by Lee et al.
"Manipulation of the rumen ecosystem to support high-performance beef cattle" by Jouany et al.
2002
"The effect of bovicin HC5, a bacteriocin from Streptococcus bovis HC5, on ruminal methane production in vitro" by Lee et al.
2003
"Possible quorum sensing in the rumen microbial community: detection of quorum-sensing signal molecules from rumen bacteria" by Mitsumori et al.
"Ionophore resistance of ruminal bacteria and its potential impact on human health" by Russell and Houlihan.
2004
"Differences in the range of faecal dry matter content between feeding types of captive wild ruminants" by Class et al.
2005
"Effects of BioChlor and Fermenten on microbial protein synthesis in continuous culture fermenters" by Lean et al.
See comment about Fermenten below in Penner et al. 2009.
2006
"Degradation of scrapie associated prion protein (PrPSc) by the gastrointestinal microbiota of cattle" by Scherbel et al.
2008
Want to know about what I call rumen microbial chemistry, with emphasis on the Archaea? You have to read this: Structure of the Archaeal Community of the Rumen by Janssen and Kirs.
"Linkage of microbial ecology to phenotype: correlation of rumen microbial ecology to cattle’s feed efficiency" by Guan et al.
This is the first paper addressing the relationship between the gut microbiota and feed efficiency in beef cattle.
2009
"Effects of feeding Fermenten on ruminal fermentation in lactating Holstein cows fed two dietary sugar concentrations" by Penner et al.
The authors mentioned that replacing canola meal and urea with Fermenten did not increase ruminal pH or nutrient digestibility although it may decrease biohydrogenation of unsaturated fatty acids in the rumen. Additionally, the authors mention that feeding Fermenten increased milk energy output for cows fed low-sugar diets, but not for cows fed high-sugar diets in the present study.
But what is Fermenten? According to the authors, Fermenten is is a byproduct of fermentation that contains a high proportion of amino acids and short peptides. In one website (https://ahfoodchain.com/species/dairy/products/fermenten_canada), it says that:
FERMENTEN™ delivers more metabolizable protein (MP). Metabolizable protein is the ideal form of protein that is digested postruminally and supplies essential amino acids to the cow.
Optimizing dietary MP has been shown to:
Help heifers grow at a rate closer to their genetic potential and reach breeding size and join the milking herd in a more efficient manner
Supports milk and component production more consistent with the ability of the cow
Consistent quality and essential nutrients for full value and repeatable results
There is another paper by Lean et al. (2005) here it says that: BioChlor and Fermenten (B/F) are products derived from by-product streams of fermentation. The products contain high concentrations (107 g/kg BioChlor and 82 g/kg Fermenten) of free AA and peptides up to 10 AA in length (T. K. Miller-Webster and W. Hoover, unpublished data, 2003). Peptides and AA provide an ideal substrate for microbial growth and increase the efficiency of microbial protein synthesis (Russell et al. 1992).
I am still not sure what exactly is Fermenten.
2011
"Long-term defaunation increases the abundance of cellulolytic ruminococci and methanogens but does not affect the bacterial and methanogen diversity in the rumen of sheep" by Mosoni et al.
Very interesting indeed. "This study shows no major difference between long- and short-term defaunation in abundance and diversity of bacteria and archaea. It also provides evidence that monitoring the abundance and diversity of methanogens is not sufficient to comprehend the microbial mechanisms leading to a reduction in methane emissions by ruminants".
"Comparison of the fecal microbiota in feral and domestic goats" by De Jesus-Laboy et al.
2012
"Composition and similarity of bovine rumen microbiota across individual animals" by Jami and Mizrahi.
This paper suggests the existence of a core microbiome in the bovine rumen; however, the authors only used 16 Israeli Holstein Friesian lactating cows. Also, the whole issues of the existence and characteristics of a core microbiome is in constant scrutiny by the global scientific community.
"Perturbation dynamics of the rumen microbiota in response to exogenous butyrate" by Li et al.
"A meta-analysis of the effects of feeding yeast culture produced by anaerobic fermentation of Saccharomyces cerevisiae on milk production of lactating dairy cows" by Poppy et al.
2013
In a complex microbial ecosystem, there are usually members of all the three main primary kingdoms (Bacteria, Archaeae and Eukarya); however, the analysis of the co-ocurrence of these three groups is not a trivial matter. In the paper entitled "Simultaneous amplicon sequencing to explore co-ocurrence patterns of bacterial, archaeal and eukaryotic microorganisms in rumen microbial communities", co-authored by Rob Knight and Jeffrey Gordon, the authors managed to explore the co-ocurrence of all the three primary kingdoms accurately, that is, by taking into account i) the abundance of each group, ii) the degree of diversity of each group, and iii) the amplicon lengths of selected marker genes. In my experience, I have never seen such an approach to accurately measure each kingdom at the same time yet separately.
"Mitigation of methane and nitrous oxide emissions from animal operations: I. A review of enteric methane mitigation options" by Hristov et al.
One of the very best review articles about the topic of methane mitigation.
"Exploring the bovine rumen bacterial community from birth to adulthood" by Jami et al.
"Plant components with specific activities against rumen methanogens" Cieslak et al.
"Low-methane yield sheep have smaller rumens and shorter rumen retention time" by Goopy et al.
"Changes in the rumen epimural bacterial diversity of beef cattle as affected by diet and induced ruminal acidosis" by Petri et al.
"Effect of DNA Extraction Methods and Sampling Techniques on the Apparent Structure of Cow and Sheep Rumen Microbial Communities" by Henderson et al.
2014
"Rumen transfaunation" by DePeters and George.
An excellent review of an ancient technique to re-establish health in ruminants.
"High-throughput methods redefine the rumen microbiome and its relationship with nutrition and metabolism" by McCann et al.
Excellent review.
2015
"Rumen microbial community composition varies with diet and host, but a core microbiome is found across a wide geographical range" by Henderson et al.
To my knowledge, and as stated by the authors, this is the largest single study to examine microbial communities across a range of ruminant and camelid species, diets, and geographical regions.
"Rumen Fungi" by Fliegerová et al.
"Ruminal Bacterial Community Composition in Dairy Cows Is Dynamic over the Course of Two Lactations and Correlates with Feed Efficiency" by Jewell et al.
2016
I may have said this about other papers but now I mean it, this paper is VERY important. "Bovine Host Genetic Variation Influences Rumen Microbial Methane Production with Best Selection Criterion for Low Methane Emitting and Efficiently Feed Converting Hosts Based on Metagenomic Gene Abundance" by Rainer Roehe et al. published in PLoS Genetics. Basically, the authors propose using the abundance of rumen microorganisms to guide genetic selection of animals for lower methane emissions.
"The importance of microbiota in ruminant production" by Alexander and Plaizier.
In this paper, the authors mentioned that "Esophageal tubing with collection of feed particles associated with the strainer provides a representative rumen sample similar to a sample collected via the rumen cannula. "
2017
"Host Immune Selection of Rumen Bacteria through Salivary Secretory IgA" by Janelle M. Fouhse et al.
Very little is known about what host factors shape rumen microbial composition. This paper shows evidence suggesting that salivary secreatory IgA-coating may be one host-derived mechanism impacting commensal microbial colonization in the rumen.
The paper cited above by Rainer Roehe in PLoS Genetics relates to a intriguing question of whether some gut microorganisms in cattle are inherited. "Heritable bovine rumen bacteria are phylogenetically related and correlated with the cow's capacity to harvest energy from its feed" by Sasson et al. is one of the very best contributions to answering this puzzle.
There is a very interesting article by Alison Van Eenennaam that discusses the question of how might DNA-based information generate value in the beef cattle sector. This article is based on a presentation given by Alison on May 29th, 2012.
"Feed efficiency phenotypes in lambs involve changes in ruminal, colonic, and small-intestine-located microbiota" by Perea et al.
This is interesting because most people interested in the relationship between feed efficiency and the gut microbiome have focused on the rumen only.
"Monensin and nisin affect rumen fermentation and microbiota differently in vitro" by Shen et al.
Figure 1 in this paper is very useful, it shows the effect of monensin and two doses of nisin on total bacteria, methanogenic archaea, protozoa and fungi.
"A Structural and Functional Elucidation of the Rumen Microbiome Influenced by Various Diets and Microenvironments" by Deusch et al.
"Fibrobacter communities in the gastrointestinal tracts of diversehindgut-fermenting herbivores are distinct from those of the rumen" by Neumann et al.
"Niacin alters the ruminal microbial composition of cattle under high-concentrate condition" by Luo et al.
"Temporal dynamics of in-situ fiber-adherent bacterial community under ruminal acidotic conditions determined by 16S rRNA gene profiling" by Petri et al.
In this paper, the authors showed interesting results about Succiniclasticum, such as negative correlations to propanoate metabolism, and that an increase in this group on high grain diets is well documented, with a reference to Henderson et al. 2015 mentioned above.
2018
"Cultivation and sequencing of rumen microbiome members from the Hungate1000 Collection" by Seshadri et al.
Among other interesting things, the authors showed that "the comparison with the human microbiome revealed rumen-specific enrichment for genes encoding de novo synthesis of vitamin B12".
"Assessment of microbiome changes after rumen transfaunation: implications on improving feed efficiency in beef cattle" by Zhou et al.
This is one of the most important papers regarding feed efficiency and rumen transfaunation. Accordingly to the authors, "only one study has been explored in dairy cows, where whole rumen content of the two donor cows was introduced to other two recipient animals". This other study was published in 2010.
"Landscape of multi-tissue global gene expression reveals the regulatory signatures of feed efficiency in beef cattle" by Sun et al.
"Review: Biological determinants of between-animal variation in feed efficiency of growing beef cattle" by Cantalapiedra-Hijar et al.
"This review aims to identify biological determinants and molecular pathways involved in the between-animal variation in feed efficiency with particular reference to growing beef cattle phenotyped for residual feed intake (RFI)".
"Addressing Global Ruminant Agricultural Challenges Through Understanding the Rumen Microbiome: Past, Present, and Future" by Huws et al.
"Insights Into Culturomics of the Rumen Microbiome" by Zehavi et al.
"Microbiome and Allergic Diseases" by Pascal et al.
"Identification, characterization and selection of autochthonous lactic acid bacteria as probiotic for feedlot cattle" by Maldonado et al.
2019
In here the authors said that "Differential rumen microbial features (e.g., taxa, diversity indices, functional categories, and genes were detected between cattle with high and low feed efficiency, and most of them were breed-specific".
"A multi-kingdom study reveals the plasticity of the rumen microbiota in response to a shift from non-grazing to grazing diets in sheep" by Belanche et al.
"Predicting residual feed intake status using rumen microbial profiles in ewe lambs" by Ellison et al.
"Effects clay mineral supplementation on particle-associated and epimural microbiota, and gene expression in the rumen of cows fed high-concentrate diet" by Neubauer et al.
"Host genetics influence the rumen microbiota and heritable rumen microbial features associate with feed efficiency in cattle" by Li et al.
This paper shows that sex is determinant to shape the bacterial and the archaeal microbiota of beef cattle.
"Temporal Stability of the Ruminal Bacterial Communities in Beef Steers" by Clemmons et al. In this paper, the authors said that "The results of this study suggest that adaptation and wash-out periods must be re-evaluated in order to accommodate necessary rumen microbiome acclimation." Also of importance, rumen content samples were collected via gastric tubing and mentioned that "Studies examining methods of oro-gastric tubing and cannulation sampling have demonstrated that oro-gastric tubing with collection of content and feed particles associated with the strainer, provides a representative rumen sample similar to a sample collected via the rumen cannula" with this reference from Paz et al. (2016).
"Islands in the stream: from individual to communal fiber degradation in the rumen ecosystem" by Sarah Moraïs and Itzhak Mizrahi.
"Colonization of the human gut by bovine bacteria present in Parmesan cheese" by Milani et al.
"Regulation of rumen development in neonatal ruminants through microbial metagenomes and host transcriptomes" by Malmuthuge et al.
"Effect of heat stress on bacterial composition and metabolism in the rumen of lactating dairy cows" by Zhao et al.
"The vaginal and fecal microbiomes are related to pregnancy status in beef heifers" by Deng et al.
"Temporal stability of the rumen microbiota in beef cattle, and response to diet and supplements" by Snelling et al.
"Bovine genome-microbiome interactions: metagenomic frontier for the selection of efficient productivity in cattle systems" by Phyllip R. Myer.
"Fecal Microbial Communities in a Large Representative Cohort of California Dairy Cows" by Hagey et al.
"Characterizing the bacterial community across the gastrointestinal tract of goats: Composition and potential function" by Wang et al.
"Effects of Dietary-SCFA on Microbial Protein Synthesis and Urinal Urea-N Excretion Are Related to Microbiota Diversity in Rumen" by Lu et al.
"Evaluation of the therapeutic efficacy of rumen transfaunation" by Steiner.
"Organic additives used in beef cattle feedlot: Effects on metabolic parameters and animal performance" by Gonçalves Leite et al.
As stated by the authors, postbiotics are the metabolites of probiotic bacteria which are characterized by probiotic effect with the absence of living cells.
"Dynamics and stabilization of the rumen microbiome in yearling Tibetan sheep" by Wang et al.
"The rumen microbiome: a crucial consideration when optimising milk and meat production and nitrogen utilisation efficiency" by Matthews et al.
"Identification of Rumen Microbial Genes Involved in Pathways Linked to Appetite, Growth, and Feed Conversion Efficiency in Cattle" by Lima et al.
2020
"Review: Comparative Methane Production in Mammalian Herbivores" by Clauss et al.
"The day-to-day stability of the ruminal and fecal microbiota in lactating dairy cows" by Huang et al.
"Digestive tract microbiota of beef cattle that differed in feed efficiency" by Freetly et al.
"Dynamic change of the gastrointestinal bacterial ecology in cows from birth to adulthood" by Guo et al.
"Metabolic Hydrogen Flows in Rumen Fermentation: Principles and Possibilities of Interventions" by Ungerfeld.
2021
"Comparative Analysis of the Microbiota Between Rumen and Duodenum of Twin Lambs Based on Diets of Ceratoides or Alfalfa" by Pazamilala Akonyani et al.
"Implication and challenges of direct-fed microbial supplementation to improve ruminant production and health" by Ban and Guan.
"Oregano Essential Oils Promote Rumen Digestive Ability by Modulating Epithelial Development and Microbiota Composition in Beef Cattle" by Zhang et al.
2022
"Stool and Ruminal Microbiome Components Associated With Methane Emission and Feed Efficiency in Nelore Beef Cattle" by Andrade et al.
"The Effects of Breed and Residual Feed Intake Divergence on the Abundance and Active Population of Rumen Microbiota in Beef Cattle" by Zhang et al.
"Fecal Microbiome Differences in Angus Steers with Differing Feed Efficiencies during the Feedlot-Finishing Phase" by Lourenco et al.
People in rumen microbiology
Robert Hungate (March 2 1906 - September 21 2004) was a pioneering microbial ecologist who developed the first techniques for the culturing of anaerobic microbes in his study of the bovine rumen.
Dr. T.G. Nagaraja has over 40 years of experience in rumen microbiology (publications in PubMed) and is a leading scientist in the field, particularly in the study of pathogenic microorganisms in cattle.
Dr. Harvey Freetly is a recognized scientist from the USDA that has written wonderful contributions to the understanding of the ruminal gut microbiota. In the article "It's not about cow's farts", Dr. Freetly explains that methane from cows comes from ruminal fermentation and expelled trough burps. He also said that increasing feed efficiency of cattle by reducing their feed intake also reduces their production of methane. Methane production increases with feed intake. Dr. Freetly has been collaborating with Dr. Phillip Mayer from the University of Tennessee.
Dr. Le Luo Guan, from the University of Alberta. She is the first and corresponding author of the first paper addressing a possible relationship between the gut microbiota and feed efficiency in beef cattle (Guan et al. 2008). After this, she and her team have published a great number of papers related to gut microbial ecology in cattle.