An Investigation into Rumen Fungal and Protozoal Diversity in Three Rumen Fractions, during High-Fiber or Grain-Induced Sub-Acute Ruminal Acidosis Conditions, with or without Active Dry Yeast Supplementation

Invited review: "Probiotic" approaches to improving dairy production: Reassessing "magic foo-foo dust"

The gastrointestinal microbial consortium in dairy cattle is critical to determining the energetic status of the dairy cow from birth through her final lactation. The ruminant's microbial community can degrade a wide variety of feedstuffs, which can affect growth, as well as production rate and efficiency on the farm, but can also affect food safety, animal health, and environmental impacts of dairy production. Gut microbial diversity and density are powerful tools that can be harnessed to benefit both producers and consumers. The incentives in the United States to develop Alternatives to Antibiotics for use in food-animal production have been largely driven by the Veterinary Feed Directive and have led to an increased use of probiotic approaches to alter the gastrointestinal microbial community composition, resulting in improved heifer growth, milk production and efficiency, and animal health. However, the efficacy of direct-fed microbials or probiotics in dairy cattle has been highly variable due to specific microbial ecological factors within the host gut and its native microflora. Interactions (both synergistic and antagonistic) between the microbial ecosystem and the host animal physiology (including epithelial cells, immune system, hormones, enzyme activities, and epigenetics) are critical to understanding why some probiotics work but others do not. Increasing availability of next-generation sequencing approaches provides novel insights into how probiotic approaches change the microbial community composition in the gut that can potentially affect animal health (e.g., diarrhea or scours, gut integrity, foodborne pathogens), as well as animal performance (e.g., growth, reproduction, productivity) and fermentation parameters (e.g., pH, short-chain fatty acids, methane production, and microbial profiles) of cattle. However, it remains clear that all direct-fed microbials are not created equal and their efficacy remains highly variable and dependent on stage of production and farm environment. Collectively, data have demonstrated that probiotic effects are not limited to the simple mechanisms that have been traditionally hypothesized, but instead are part of a complex cascade of microbial ecological and host animal physiological effects that ultimately impact dairy production and profitability.

Investigating the effect of supplementing different levels of Isochrysis galbana on in vitro rumen fermentation parameters

This study aimed to investigate the effect of supplementing Isochrysis galbana (I. galbana) at levels of 0 (control), 1, 2, 3, 4, and 5 (g/100 g DM) of the diet on the gas production kinetics, methane production, rumen fermentation parameters, and relative microbial population in vitro. Supplementation of I. galbana at high level (5 g/100 g DM) caused a significant decrease in total gas production (p < 0.05). High supplementation rates (4 and 5 g/100 g DM) decreased CH4 production relative to the control by 18.4% and 23.2%, respectively. Although rumen ammonia nitrogen (N-NH3) and total volatile fatty acids (VFA) concentrations were affected by dietary treatments, but the VFA profile did not changed. The relative proportion of protozoa and methanogenic archaea as well as Anaerovibrio lipolytica, Prevotella spp., Ruminococcus flavefaciens, and Fibrobacter succinogenes were decreased significantly as a result of microalgae supplementation. However, the relative abundance of Ruminococcus albus, Butyrivibrio fibrisolvens and Selenomonas ruminantium were significantly increased (p < 0.05), related to the control group. As well, the pH was not affected by dietary treatments. It was concluded that I. galbana reduced in vitro CH4 production and methanogenic archaea that its worth to be investigated further in in vivo studies.

Transmission of fungi and protozoa under grazing conditions from lactating yaks to sucking yak calves in early life

Microbiota from mothers is an essential source of microbes in early-life rumen microbiota, but the contribution of microbiota from different maternal sites to the rumen microbiota establishment in neonates needs more data. To fill this gap, we collected samples from the mouth, teat skin, and rumen of lactating yaks and from the rumen of sucking calves concomitantly on seven occasions between days 7 and 180 after birth under grazing conditions. We observed that the eukaryotic communities clustered based on sample sites, except for the protozoal community in the teat skin, with negative correlations between fungal and protozoal diversities in the rumen of calves. Furthermore, fungi in the dam's mouth, which is the greatest source of the calf's rumen fungi, accounted for only 0.1%, and the contribution of the dam's rumen to the calf's rumen fungi decreased with age and even disappeared after day 60. In contrast, the average contribution of the dam's rumen protozoa to the calf's rumen protozoa was 3.7%, and the contributions from the dam's teat skin (from 0.7 to 2.7%) and mouth (from 0.4 to 3.3%) increased with age. Thus, the divergence in dam-to-calf transmissibility between fungi and protozoa indicates that the foundation of these eukaryotic communities is shaped by different rules. This study provides the first measurements of the maternal contribution to the fungal and protozoal establishment in the rumen of sucking and grazing yak calves in early life, which could be beneficial for future microbiota manipulation in neonatal ruminants. KEY POINTS: • Dam to calf transfer of rumen eukaryotes occurs from multiple body sites. • A minor proportion of rumen fungi in calves originated from maternal sites. • The inter-generation transmission between rumen fungi and protozoa differs.

Effects on rumen pH and feed intake of a dietary concentrate challenge in cows fed rations containing pH modulators with different neutralizing capacity

Forty-five Holstein lactating cows (41 ± 8.8 kg/d of milk yield, 96 ± 35.6 days in milk, and 607 ± 80.4 kg of body weight) were enrolled in this study to assess the effects of diets supplemented with sodium bicarbonate or a magnesium-based product and their corresponding differences in dietary cation-anion difference (DCAD) on rumen pH, rumen microbial population, and milk performance of dairy cattle exposed to an induced decrease in rumen pH through a dietary challenge. Cows were randomly allocated to 3 total mixed rations (TMR) differing in the type of supplement to modulate rumen pH: (1) control, no supplementation; (2) SB, supplemented with 0.82% of sodium bicarbonate with a neutralizing capacity (NC) of 12 mEq/g; and (3) MG, supplemented with 0.25% of magnesium oxide (pHix-Up, Timab Magnesium) with a NC of 39 mEq/g. Thus, SB and MG rations had, in theory, the same NC. The 3 TMR differed for control, SB, and MG in their DCAD-S (calculated considering Na, K, Cl, and S), which was on average 13.2, 21.2, and 13.7 mEq/100 g, respectively, or DCAD-Mg (calculated accounting for Mg, Ca, and P), which was 31.4, 41.2, and 35.2 mEq/100 g, respectively. The study lasted 63 d, with the first 7 d serving as a baseline, followed by a fortnightly progressive decrease of dietary forage-to-concentrate ratio (FCR) starting at 48:52, then 44:56, then 40:60, and finishing at 36:64. Individual dry matter intake (DMI) was recorded daily. Seven cows per treatment were equipped with electronic rumen boluses to monitor rumen pH. Control and SB cows consumed less dry matter (DM; 23.5 ± 0.31 kg/d) than MG cows (25.1 ± 0.31 kg/d) when fed dietary FCR of 44:56 and 40:60. Energy-corrected milk decreased from 40.8 ± 1.21 to 39.5 ± 1.21 kg/d as dietary FCR decreased, independently of dietary treatments. Rumen pH decreased and the proportion of the day with rumen pH <5.8 increased as dietary FCR decreased, and at low dietary FCR (i.e., 36:64) rumen pH was greater in MG cows than in control and SB cows. Reducing the DCAD-S from 28 to 18 mEq/100 g or the DCAD-Mg from 45 to 39 mEq/kg had no effects on DMI or milk yield. Cows supplemented with ∼62 g/d of magnesium oxide (pHix-Up) maintained a greater rumen pH and consumed more DM than cows supplemented with ∼200 g/d of sodium bicarbonate when fed a diet with low FCR.

The Colonization of Rumen Microbiota and Intervention in Pre-Weaned Ruminants

In pre-weaned ruminants, the microbiota colonizes rapidly in the rumen after birth and constantly interacts with the host to sustain health and metabolism. The developing microbial community is more malleable, so its manipulation may improve ruminant health and productivity as well as may have long-term effects on ruminants. Hence, understanding the process of rumen microbiota establishment is helpful for nutritional interventions of rumen microbiota in pre-weaned ruminants. This paper reviews the latest advances in the colonization of rumen microbiota while providing insights into the most suitable time for manipulating rumen microbial colonization in early life. In addition, different factors that affect rumen microbiota establishment during the pre-weaned ruminants are discussed in the current manuscript. The purpose of this review is to aid in the development of guidelines for manipulating rumen microbiota to improve animal productivity and health.

The Effect of Combining Millet and Corn Straw as Source Forage for Beef Cattle Diets on Ruminal Degradability and Fungal Community

Three ruminal cannulated Simmental crossbreed bulls (approximately 3 years of age and with 380 ± 20 kg live weight at initiation of the experiment) were used in a 3 × 3 Latin square experiment in order to determine the effects of the treatments on ruminal pH and degradability of nutrients, as well as the rumen fungal community. The experimental periods were 21 d, with 18 d of adjustment to the respective dietary treatments and 3 d of sample collection. Treatments consisted of a basal diet containing a 47.11% composition of two sources of forage as follows: (1) 100% millet straw (MILLSTR), (2) 50:50 millet straw and corn straw (COMB), and (3) 100% corn straw (CORNSTR). Dry matter (DM), crude protein (CP), neutral detergent fiber (NDF), and acid detergent fiber (ADF) were tested for ruminal degradability using the nylon bag method, which was incubated for 6, 12, 24, 36, 48, and 72 h, and rumen fungal community in rumen fluid was determined by high-throughput gene sequencing technology. Ruminal pH was not affected by treatments. At 72 h, compared to MILLSTR, DM degradability of CORNSTR was 4.8% greater (p < 0.05), but when corn was combined with millet straw, the difference in DM degradability was 9.4%. During the first 24 h, degradability of CP was lower for CORNSTR, intermediate for MILLSTR, and higher for COMB. However, at 72 h, MILLSTR and COMB had a similar CP degradability value, staying greater than the CP degradability value of the CORNSTR treatment. Compared to MILLSTR, the rumen degradability of NDF was greater for CORNSTR and intermediate for the COMB. There was a greater degradability for ADF in CORNSTR, intermediate for COMB, and lower for MILLSTR. In all treatments, Ascomycota and Basidiomycota were dominant flora. Abundance of Basidiomycota in the group COMB was higher (p < 0.05) than that in the group CORNSTR at 12 h. Relative to the fungal genus level, the Thelebolus, Cladosporium, and Meyerozyma were the dominant fungus, and the abundance of Meyerozyma in COMB and CORNSTR were greater (p < 0.05) than MILLSTR at 12, 24, and 36 h of incubation. In conclusion, it is suggested to feed beef cattle with different proportions of millet straw and corn straw combinations.

Active dry yeast supplementation benefits ruminal fermentation, bacterial community, blood immunoglobulins, and growth performance in young dairy goats, but not for intermittent supplementation

This study evaluated the effects of active dry yeast (ADY) supplementation and supplementation strategies on ruminal fermentation, bacterial community, blood metabolites, and growth performance in young dairy goats. Sixty young female Guanzhong dairy goats of similar age (4.00 ± 0.50 months) and BW (19.65 ± 0.41 kg) were randomly divided into 3 groups (n = 20): (1) basal diet group (CON); (2) basal diet continuously supplemented with 3.0 g/goat per day commercial ADY (a proprietary strain of Saccharomyces cerevisiae with 5.0 × 10⁹ cfu/g) group (CSY); (3) basal diet with intermittently supplemented ADY group (ISY; 5 d supplementation with ADY at 4.5 g/goat per day following 5 d of no supplementation). The experiment lasted 67 d with the first 7 d as an adaptive period. Rumen fluid and blood samples were collected bi-weekly. Data were analyzed using the MIXED procedure combined with the SLICE option in SAS. Specific orthogonal contrasts of ADY vs. CON and CSY vs. ISY were also analyzed. During the experimental period, ADY supplementation resulted in greater DMI (P = 0.03), ruminal acetate proportion (P < 0.01) and acetylesterase activity (P = 0.01), and blood contents of glucose (P = 0.01) and IgM (P = 0.02) and tended to have greater ADG (P = 0.05) and paunch girth (P = 0.06) than the CON, despite the propionate proportion (P = 0.03) and contents of total protein (P = 0.04) and IgA (P = 0.03) being lower. The lower ruminal NH₃-N (P < 0.01) and blood urea nitrogen (P = 0.07) contents indicated greater nitrogen utilization with ADY supplementation. ADY supplementation showed persistent effects after it was stopped because the BW at 12 months of age (P = 0.03) and birth weight of lambs (P = 0.02) were greater than the CON. However, the ISY did not show those benefits and had significantly lower relative abundances of fiber-degrading related bacteria than the CSY. In conclusion, ADY supplementation, especially continuously supplemented, may enhance ADG and ADG:DMI ratio by improving DMI, ruminal cellulolytic bacteria abundance and enzyme activity, nitrogen utilization, and immune status. These findings provide a theoretical basis for the rational application of ADY and have important practical implications for the design of nutritional strategies in growing dairy goats.

Isolation and Characterization of Ruminal Yeast Strain with Probiotic Potential and Its Effects on Growth Performance, Nutrients Digestibility, Rumen Fermentation and Microbiota of Hu Sheep

Yeast strains are widely used in ruminant production. However, knowledge about the effects of rumen native yeasts on ruminants is limited. Therefore, this study aimed to obtain a rumen native yeast isolate and investigate its effects on growth performance, nutrient digestibility, rumen fermentation and microbiota in Hu sheep. Yeasts were isolated by picking up colonies from agar plates, and identified by sequencing the ITS sequences. One isolate belonging to Pichia kudriavzevii had the highest optical density among these isolates obtained. This isolate was prepared to perform an animal feeding trial. A randomized block design was used for the animal trial. Sixteen Hu sheep were randomly assigned to the control (CON, fed basal diet, n = 8) and treatment group (LPK, fed basal diet plus P. kudriavzevii, CFU = 8 × 10⁹ head/d, n = 8). Sheep were housed individually and treated for 4 weeks. Compared to CON, LPK increased final body weight, nutrient digestibility and rumen acetate concentration and acetate-to-propionate ratio in sheep. The results of Illumina MiSeq PE 300 sequencing showed that LPK increased the relative abundance of lipolytic bacteria (Anaerovibrio spp. and Pseudomonas spp.) and probiotic bacteria (Faecalibacterium spp. and Bifidobacterium spp.). For rumen eukaryotes, LPK increased the genera associated with fiber degradation, including protozoan Polyplastron and fungus Pichia. Our results discovered that rumen native yeast isolate P. kudriavzevii might promote the digestion of fibers and lipids by modulating specific microbial populations with enhancing acetate-type fermentation.

Subacute ruminal acidosis in dairy herds: Microbiological and nutritional causes, consequences, and prevention strategies

Dairy cattle are frequently fed high-concentrate (HC) diets in modern intensive feeding systems, especially in the transition period. During this period, cows face many alterations that include hormonal changes and shifting to a lactating state. Switching to a HC diet that may disrupt the ruminal microbiota balance can lead to subacute ruminal acidosis (SARA). Moreover, the main factor shaping the rumen microbiota is dietary composition, especially the ratio of starch to fibrous carbohydrates. Feeding highly fermentable carbohydrate diets after adaptation to forage diets leads to a rumen fermentation rate that exceeds rumen absorption and buffering rates, resulting in a reduction in ruminal pH. As a result of Gram-negative bacterial cell lysis, an increase in harmful ruminal bacterial metabolites, including lipopolysaccharide, lactic acid, and histamine, is observed. The interactions between the host immune system and the ruminal microbiota play an essential role in many physiological processes and the development of the disorder. Progress in DNA sequencing and bioinformatics platforms provides new opportunities to investigate the composition of ruminal microbes and yields unique advances in understanding ecology of the rumen. Subacute ruminal acidosis is linked with a change in the ruminal microbiota structure and richness and with other metabolic disorders; such as rumenitis, milk fat depression, laminitis, and liver abscesses. Therefore, this review aims to explore a better understanding of the crosstalk between diet and microbiota in the prevalence of rumen acidosis and its consequences, which is crucial for control strategies such as feeding management, and supplementation with thiamine, prebiotics, and probiotics.

The effects of feeding rations that differ in neutral detergent fiber and starch within a day on the daily pattern of key rumen microbial populations

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Rumen microbial relative abundance follows a daily pattern.

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Feeding 2 diets differing in starch and neutral detergent fiber (NDF) modifies microbial daily pattern.

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Streptococcus bovis and Butyrivibrio peaked before feeding of a high-NDF diet in the morning.

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Ruminococcus albus, Selenomonas ruminantium, and Fibrobacter succinogenes increased before feeding a low NDF diet.

The effect of feeding a single TMR versus multiple rations across the day that differ in concentrations of neutral detergent fiber (NDF) and starch on the daily pattern of rumen microbial populations was characterized. Diets included a control total mixed ration (CON; 33.3% NDF), a low-fiber diet (LF; 29.6% NDF), and a high-fiber diet (HF; 34.8% NDF). Nine cannulated Holstein cows were assigned to 1 of 3 treatment sequences in a 3 × 3 Latin square design. Treatments included feeding CON ad libitum at 0900 h, feeding HF at 70% of daily offering at 0900 h and LF at 30% of daily offering at 2200 h (H/L), and feeding LF at 30% of daily offering at 0900 h and HF at 70% of daily offering at 1300 h (L/H). Rumen digesta was collected to represent every 3 h across the day, microbial DNA was extracted, and real-time quantitative PCR was used to determine the relative abundances of total bacteria, total fungi, total protozoa, Butyrivibrio fibrisolvens, Butyrivibrio hungatei, Fibrobacter succinogenes, Megasphaera elsdenii, Prevotella bryantii, Ruminococcus albus, Selenomonas ruminantium, and Streptococcus bovis. The relative abundances of total bacteria, total ciliated protozoa, F. succinogenes, P. bryantii, R. albus, S. ruminantium, and Strep. bovis were affected by time of day. Additionally, treatment affected the relative abundance of certain microbial groups at specific times of day. Notably, H/L treatment dramatically increased the relative abundances of B. fibrisolvens, B. hungatei, and Strep. bovis at 0900 h, by 2.5-, 5.4-, and 4.4-fold, respectively. Furthermore, the relative abundances of B. hungatei (3.9-fold), M. elsdenii (3.9-fold), R. albus (1.3-fold), S. ruminantium (1.3-fold), and Strep. bovis (4.5-fold) were greatly increased by L/H at 0900 h. At 0600 h, the relative abundance of F. succinogenes was 58% greater in L/H than H/L and the relative abundance of P. bryantii was 49% greater in H/L than L/H. Results suggest that there is a daily pattern of selected microbial populations that is altered by feeding rations that differ in NDF and starch within a day, with the greatest difference occurring before morning feeding.

The Present Role and New Potentials of Anaerobic Fungi in Ruminant Nutrition

The ruminal microbiota allows ruminants to utilize fibrous feeds and is in the limelight of ruminant nutrition research for many years. However, the overwhelming majority of investigations have focused on bacteria, whereas anaerobic fungi (AF) have been widely neglected by ruminant nutritionists. Anaerobic fungi are not only crucial fiber degraders but also important nutrient sources for the host. This review summarizes the current findings on AF and, most importantly, discusses their new application potentials in modern ruminant nutrition. Available data suggest AF can be applied as direct-fed microbials to enhance ruminal fiber degradation, which is indeed of interest for high-yielding dairy cows that often show depressed ruminal fibrolysis in response to high-grain feeding. Moreover, these microorganisms have relevance for the nutrient supply and reduction of methane emissions. However, to reach AF-related improvements in ruminal fiber breakdown and animal performance, obstacles in large-scale AF cultivation and applicable administration options need to be overcome. At feedstuff level, silage production may benefit from the application of fungal enzymes that cleave lignocellulosic structures and consequently enable higher energy exploitation from forages in the rumen. Concluding, AF hold several potentials in improving ruminant feeding and future research efforts are called for to harness these potentials.

A multi-kingdom metabarcoding study on cattle grazing Alpine pastures discloses intra-seasonal shifts in plant selection and faecal microbiota

Diet selection by grazing livestock may affect animal performance as well as the biodiversity of grazed areas. Recent DNA barcoding techniques allow to assess dietary plant composition in faecal samples, which may be additionally integrated by the description of gut microbiota. In this high throughput metabarcoding study, we investigated the diversity of plant, fungal and bacterial taxa in faecal samples of lactating cows of two breeds grazing an Alpine semi-natural grassland during summer. The estimated plant composition of the diet comprised 67 genera and 39 species, which varied remarkably during summer, suggesting a decline of the diet forage value with the advancing of the vegetative season. The fungal community included Neocallimastigomycota gut symbionts, but also Ascomycota and Basidiomycota plant parasite and coprophilous taxa, likely ingested during grazing. The proportion of ingested fungi was remarkably higher than in other studies, and varied during summer, although less than that observed for plants. Some variation related to breed was also detected. The gut bacterial taxa remained stable through the summer but displayed a breed-specific composition. The study provided insights in the reciprocal organisms' interactions affecting, and being affected by, the foraging behaviour: plants showed a high temporal variation, fungi a smaller one, while bacteria had practically none; conversely, the same kingdoms showed the opposite gradient of variation as respect to the animal host breed, as bacteria revealed to be the group mostly characterized by host-specificity.

The Effect of a High-Grain Diet on the Rumen Microbiome of Goats with a Special Focus on Anaerobic Fungi

This work investigated the changes of the rumen microbiome of goats switched from a forage to a concentrate diet with special attention to anaerobic fungi (AF). Female goats were fed an alfalfa hay (AH) diet (0% grain; n = 4) for 20 days and were then abruptly shifted to a high-grain (HG) diet (40% corn grain, 60% AH; n = 4) and treated for another 10 days. Rumen content samples were collected from the cannulated animals at the end of each diet period (day 20 and 30). The microbiome structure was studied using high-throughput sequencing for bacteria, archaea (16S rRNA gene) and fungi (ITS2), accompanied by qPCR for each group. To further elucidate unclassified AF, clone library analyses were performed on the ITS1 spacer region. Rumen pH was significantly lower in HG diet fed goats, but did not induce subacute ruminal acidosis. HG diet altered prokaryotic communities, with a significant increase of Bacteroidetes and a decrease of Firmicutes. On the genus level Prevotella 1 was significantly boosted. Methanobrevibacter and Methanosphaera were the most abundant archaea regardless of the diet and HG induced a significant augmentation of unclassified Thermoplasmatales. For anaerobic fungi, HG triggered a considerable rise in Feramyces observed with both ITS markers, while a decline of Tahromyces was detected by ITS2 and decrease of Joblinomyces by ITS1 only. The uncultured BlackRhino group revealed by ITS1 and further elucidated in one sample by LSU analysis, formed a considerable part of the AF community of goats fed both diets. Results strongly indicate that the rumen ecosystem still acts as a source for novel microorganisms and unexplored microbial interactions and that initial rumen microbiota of the host animal considerably influences the reaction pattern upon diet change.

The Impact of Inulin and a Novel Synbiotic (Yeast Saccharomyces cerevisiae Strain 1026 and Inulin) on the Development and Functional State of the Gastrointestinal Canal of Calves

Successful management of the dairy industry is closely related to rearing healthy calves. The proper development of the gastrointestinal canal is crucial to reach this goal. One of the strategies to promote this development is the addition of feed additives to the diet. This research aimed to determine the impact of prebiotic inulin and a new, not commercially available synbiotic (mix of prebiotic inulin and probiotic S. cerevisiae strain 1026) on the development of the gastrointestinal canal of calves by comparing the weight of the stomach, its relative ratio to body weight and evaluating pH, and histological changes in different parts of the gastrointestinal canal and assess whether or not the addition of inulin to the yeast S. cerevisiae improves the abovementioned parameters. We used prebiotic inulin (6 g) and a synbiotic (prebiotic inulin 6 g and probiotic Saccharomyces cerevisiae strain 1026, 5 g). The 56-day long research was conducted with fifteen crossbreed calves (32 ± 6 days old) organized in the control group (CoG), the prebiotic group (PreG), and the synbiotic group (SynG). We determined pH, morphological parameters of different parts of the digestive canal, and morphometric parameters of the stomach. The addition of prebiotic inulin to calves' diet causes the increase of pH in rumen, abomasum, and intestines but when inulin was added to S. cerevisiae, pH decreased and was even lower than in the control group. Prebiotic inulin and its synbiotic with yeast S. cerevisiae positively impact the development of almost all morphological structures of rumen saccus dorsalis, rumen saccus ventralis, and intestine; moreover, calves from the synbiotic group showed better results in virtually all parameters. However, both inulin and synbiotic did not affect the weight and relative weight of different parts of the stomach. Tested synbiotic has the potential to promote the development of the rumen and other parts of the digestive canal of calves.

Anaerobic Fungi: Past, Present, and Future

Anaerobic fungi (AF) play an essential role in feed conversion due to their potent fiber degrading enzymes and invasive growth. Much has been learned about this unusual fungal phylum since the paradigm shifting work of Colin Orpin in the 1970s, when he characterized the first AF. Molecular approaches targeting specific phylogenetic marker genes have facilitated taxonomic classification of AF, which had been previously been complicated by the complex life cycles and associated morphologies. Although we now have a much better understanding of their diversity, it is believed that there are still numerous genera of AF that remain to be described in gut ecosystems. Recent marker-gene based studies have shown that fungal diversity in the herbivore gut is much like the bacterial population, driven by host phylogeny, host genetics and diet. Since AF are major contributors to the degradation of plant material ingested by the host animal, it is understandable that there has been great interest in exploring the enzymatic repertoire of these microorganisms in order to establish a better understanding of how AF, and their enzymes, can be used to improve host health and performance, while simultaneously reducing the ecological footprint of the livestock industry. A detailed understanding of AF and their interaction with other gut microbes as well as the host animal is essential, especially when production of affordable high-quality protein and other animal-based products needs to meet the demands of an increasing human population. Such a mechanistic understanding, leading to more sustainable livestock practices, will be possible with recently developed -omics technologies that have already provided first insights into the different contributions of the fungal and bacterial population in the rumen during plant cell wall hydrolysis.

Effects of Replacing Extruded Maize by Dried Citrus Pulp in a Mixed Diet on Ruminal Fermentation, Methane Production, and Microbial Populations in Rusitec Fermenters

Citrus pulp is a highly abundant by-product of the citrus industry. The aim of this study was to assess the effects of replacing extruded maize (EM; 20% of total diet) by dried citrus pulp (DCP; 20%) in a mixed diet on rumen fermentation and microbial populations in Rusitec fermenters. The two diets contained 50% alfalfa hay and 50% concentrate, and the same protein level. Four Rusitec fermenters were used in a cross-over design with two 13-d incubation runs. After 7-d of diet adaptation, diet disappearance, fermentation parameters, microbial growth, and microbial populations were assessed. Fermenters receiving the DCP showed greater pH values and fiber disappearance (p < 0.001) and lower methane production (p = 0.03) than those fed EM. Replacing EM by DCP caused an increase in the proportions of propionate and butyrate (p < 0.001) and a decrease in acetate (p = 0.04). Microbial growth, bacterial diversity, and the quantity of bacteria and protozoa DNA were not affected by the diet, but the relative abundances of fungi and archaea were greater (p < 0.03) in solid and liquid phases of DCP fermenters, respectively. Results indicate that DCP can substitute EM, promoting a more efficient ruminal fermentation.

Beef cattle that respond differently to fescue toxicosis have distinct gastrointestinal tract microbiota

Tall fescue (Lolium arundinaceum) is a widely used forage grass which shares a symbiosis with the endophytic fungus Epichloë coenophiala. The endophyte produces an alkaloid toxin that provides herbivory, heat and drought resistance to the grass, but can cause fescue toxicosis in grazing livestock. Fescue toxicosis can lead to reduced weight gain and milk yields resulting in significant losses to the livestock industry. The objective of this study was to identify bacterial and fungal communities associated with fescue toxicosis tolerance. In this trial, 149 Angus cows across two farms were continuously exposed to toxic, endophyte-infected, fescue for a total of 13 weeks. Of those 149 cows, 40 were classified into either high (HT) or low (LT) tolerance groups according to their growth performance (weight gain). 20 HT and 20 LT cattle balanced by farm were selected for amplicon sequencing to compare the fecal microbiota of the two tolerance groups. This study reveals significantly (q<0.05) different bacterial and fungal microbiota between HT and LT cattle, and indicates that fungal phylotypes may be important for an animal’s response to fescue toxicosis: We found that fungal phylotypes affiliating to the Neocallimastigaceae, which are known to be important fiber-degrading fungi, were consistently more abundant in the HT cattle. Whereas fungal phylotypes related to the genus Thelebolus were more abundant in the LT cattle. This study also found more pronounced shifts in the microbiota in animals receiving higher amounts of the toxin. We identified fungal phylotypes which were consistently more abundant either in HT or LT cattle and may thus be associated with the respective animal’s response to fescue toxicosis. Our results thus suggest that some fungal phylotypes might be involved in mitigating fescue toxicosis.

Microbial patterns in rumen are associated with gain of weight in beef cattle

Ruminal microorganisms play a pivotal role in cattle nutrition. The discovery of the main microbes or of a microbial community responsible for enhancing the gain of weight in beef cattle might be used in therapeutic approaches to increase animal performance and cause less environmental damages. Here, we examined the differences in bacterial and fungal composition of rumen samples of Braford heifers raised in natural grassland of the Pampa Biome in Brazil. We aimed to detect microbial patterns in the rumen that could be correlated with the gain of weight. We hypothesized that microorganisms important to digestion process are increased in animals with a higher gain of weight. The gain of weight of seventeen healthy animals was monitored for 60 days. Ruminal samples were obtained and the 16S and ITS1 genes were amplified and sequenced to identify the closest microbial relatives within the microbial communities. A predictive model based on microbes responsible for the gain of weight was build and further tested using the entire dataset., The main differential abundant microbes between groups included the bacterial taxa RFN20, Prevotella, Anaeroplasma and RF16 and the fungal taxa Aureobasidium, Cryptococcus, Sarocladium, Pleosporales and Tremellales. The predictive model detected some of these taxa associated with animals with the high gain of weight group, most of them being organisms that have been correlated to the production of substances that improve the ruminal digestion process. These findings provide new insights about cattle nutrition and suggest the use of these microbes to improve beef cattle breeding.

Exploring the eukaryotic diversity in rumen of Indian camel (Camelus dromedarius) using 18S rRNA amplicon sequencing

In addition to a wide variety of anaerobic and facultative anaerobic bacteria, camel rumen also harbors a diverse of eukaryotic organisms. In the present study, the eukaryotic communities of camel rumen were characterized using 18S rRNA amplicon sequencing. Metagenomic DNA was isolated from rumen samples of fourteen adult Bikaneri and Kachchhi breeds of camel fed different diets containing Jowar, Bajra, Maize, and Guar. Illumina sequencing generated 27,161,904 number of reads corresponding to 1543 total operational taxonomic units (OTUs). Taxonomic classification of community metagenome sequences from all the samples revealed the presence of 92 genera belonging to 16 different divisions, out of which Ciliophora (73%), Fungi (13%) and Streptophyta (9%) were found to be the most dominant. Notably, the abundance of Ciliophora was significantly higher in the case of Guar feed, while Fungi was significantly higher in the case of Maize feed, indicating the influence of cellulose and hemicellulose content of feedstuff on the composition of eukaryotes. The results suggest that the camel rumen eukaryotes are highly dynamic and depend on the type of diet given to the animal. Pearson's correlation analysis suggested the ciliate protozoa and fungi were negatively correlated with each other. To the best of our knowledge, this is first systematic study to characterize camel rumen eukaryotes, which has provided newer information regarding eukaryotic diversity patterns amongst camel fed on different diets.

Extending Burk Dehority's Perspectives on the Role of Ciliate Protozoa in the Rumen

Dr. Burk Dehority was an international expert on the classification and monoculture of ruminal ciliated protozoa. We have summarized many of the advancements in knowledge from his work but also in his scientific way of thinking about interactions of ruminal ciliates with the entire rumen microbial community and animal host. As a dedication to his legacy, an electronic library of high-resolution images and video footage catalogs numerous species and techniques involved in taxonomy, isolation, culture, and ecological assessment of ruminal ciliate species and communities. Considerable promise remains to adapt these landmark approaches to harness eukaryotic cell signaling technology with genomics and transcriptomics to assess cellular mechanisms regulating growth and responsiveness to ruminal environmental conditions. These technologies can be adapted to study how protozoa interact (both antagonism and mutualism) within the entire ruminal microbiota. Thus, advancements and limitations in approaches used are highlighted such that future research questions can be posed to study rumen protozoal contribution to ruminant nutrition and productivity.

Manipulating the rumen microbiome to address challenges facing Australasian dairy farming

As dairy production systems expand globally, there is an increasing need to reduce the impact of dairy wastes on the environment by decreasing urinary N output and reducing emissions of green-house gasses (GHG). An understanding of rumen microbiome composition can result in the development of strategies that reduce methane emissions and nitrogen leakage, ultimately lowering the impact of dairying on the environment, while improving animal productivity. The strongest driver of the composition of the rumen microbiome was found to be the diet of the host animal. Thus, dietary manipulation offers a viable solution to alter the microbiome to address present-day challenges faced by the dairy industry. In the present review, we discuss such strategies and provide insight into rumen microbiome changes that have resulted in reduced GHG emissions and improved animal productivity.

Metatranscriptomics reveals mycoviral populations in the ovine rumen

The rumen is known to contain DNA-based viruses, although it is not known whether RNA-based viruses that infect fungi (mycoviruses) are also present. Analysis of publicly available rumen metatranscriptome sequence data from sheep rumen samples (n = 20) was used to assess whether RNA-based viruses exist within the ovine rumen. A total of 2466 unique RNA viral contigs were identified that had homology to nine viral families. The Partitiviridae was the most consistently observed mycoviral family. High variation in the abundance of each detected mycovirus suggests that rumen mycoviral populations vary greatly between individual sheep. Functional analysis of the genes within the assembled mycoviral contigs suggests that the mycoviruses detected had simple genomes, often only carrying the machinery required for replication. The fungal population of the ovine rumen was also assessed using metagenomics data from the same samples, and was consistently dominated by the phyla Ascomycota and Basidomycota. The strictly anaerobic phyla Neocallimastigomycota were also present in all samples but at a low abundance. This preliminary investigation has provided clear evidence that mycoviruses with RNA genomes exist in the rumen, with further in-depth studies now required to characterise this mycoviral community and determine its role in the rumen.

Review: Are there indigenous Saccharomyces in the digestive tract of livestock animal species? Implications for health, nutrition and productivity traits

All livestock animal species harbour complex microbial communities throughout their digestive tract that support vital biochemical processes, thus sustaining health and productivity. In part as a consequence of the strong and ancient alliance between the host and its associated microbes, the gut microbiota is also closely related to productivity traits such as feed efficiency. This phenomenon can help researchers and producers develop new and more effective microbiome-based interventions using probiotics, also known as direct-fed microbials (DFMs), in Animal Science. Here, we focus on one type of such beneficial microorganisms, the yeast Saccharomyces. Saccharomyces is one of the most widely used microorganisms as a DFM in livestock operations. Numerous studies have investigated the effects of dietary supplementation with different species, strains and doses of Saccharomyces (mostly Saccharomyces cerevisiae) on gut microbial ecology, health, nutrition and productivity traits of several livestock species. However, the possible existence of Saccharomyces which are indigenous to the animals' digestive tract has received little attention and has never been the subject of a review. We for the first time provide a comprehensive review, with the objective of shedding light into the possible existence of indigenous Saccharomyces of the digestive tract of livestock. Saccharomyces cerevisiae is a nomadic yeast able to survive in a broad range of environments including soil, grass and silages. Therefore, it is very likely that cattle and other animals have been in direct contact with this and other types of Saccharomyces throughout their entire existence. However, to date, the majority of animal scientists seem to agree that the presence of Saccharomyces in any section of the gut only reflects dietary contamination; in other words, these are foreign organisms that are only transiently present in the gut. Importantly, this belief (i.e. that Saccharomyces come solely from the diet) is often not well grounded and does not necessarily hold for all the many other groups of microbes in the gut. In addition to summarizing the current body of literature involving Saccharomyces in the digestive tract, we discuss whether the beneficial effects associated with the consumption of Saccharomyces may be related to its foreign origin, though this concept may not necessarily satisfy the theories that have been proposed to explain probiotic efficacy in vivo. This novel review may prove useful for biomedical scientists and others wishing to improve health and productivity using Saccharomyces and other beneficial microorganisms.

Zinc AA supplementation alters yearling ram rumen bacterial communities but zinc sulfate supplementation does not

 Despite the body of research into Zn for human and animal health and productivity, very little work has been done to discern whether this benefit is exerted solely on the host organism, or whether there is some effect of dietary Zn upon the gastrointestinal microbiota, particularly in ruminants. We hypothesized that (i) supplementation with Zn would alter the rumen bacterial community in yearling rams, but that (ii) supplementation with either inorganically sourced ZnSO4, or a chelated Zn AA complex, which was more bioavailable, would affect the rumen bacterial community differently. Sixteen purebred Targhee yearling rams were utilized in an 84-d completely randomized design, and allocated to one of three pelleted dietary treatments: control diet without fortified Zn (~1 × NRC), a diet fortified with a Zn AA complex (~2 × NRC), and a diet fortified with ZnSO4 (~2 × NRC). Rumen bacterial community was assessed using Illumina MiSeq of the V4 to V6 region of the 16S rRNA gene. One hundred and eleven OTUs were found with > 1% abundance across all samples. The genera Prevotella, Solobacterium, Ruminococcus, Butyrivibrio, Olsenella, Atopobium, and the candidate genus Saccharimonas were abundant in all samples. Total rumen bacterial evenness and diversity in rams were reduced by supplementation with a Zn AA complex, but not in rams supplemented with an equal concentration of ZnSO4, likely due to differences in bioavailability between organic and inorganically sourced supplement formulations. A number of bacterial genera were altered by Zn supplementation, but only the phylum Tenericutes was significantly reduced by ZnSO4 supplementation, suggesting that either Zn supplementation formulation could be utilized without causing a high-level shift in the rumen bacterial community which could have negative consequences for digestion and animal health.

Are We Overestimating Protistan Diversity in Nature?

Documenting the immense diversity of single-celled, eukaryotic organisms (protists) has been a formidable challenge for ecologists. These species were originally defined by morphological criteria, but shortcomings of the morphospecies concept, and a bewildering array of sizes and cellular attributes, has made constructing a taxonomy that is useful for ecologists nearly impossible. Consequently, physiological and genetic information has been integrated to address these shortcomings, and to develop the framework of a unifying taxonomy. DNA sequence information, in particular, has revolutionized studies of protistan diversity. However, the exponential increase in sequence-based protistan species richness published from field surveys in recent years raises the question of whether we have moved beyond characterizing species-level diversity and begun to reveal intraspecies diversity. The answer to that question appears to be 'yes', at least for some protistan lineages. The need to document such microdiversity may be justified, but it is important for protistologists to recognize and acknowledge that possibility, and its consequences.

Community structure and fibrolytic activities of anaerobic rumen fungi in dromedary camels

Anaerobic fungi colonize the rumen and degrade cellulose and hemicellulose, which enable them to be key players in the lignocellulose fermentation. Consequently, an expansion of knowledge about rumen fungi could increase animal productivity, utilization of lignified forages like alfalfa hay, and enhance fibrolytic enzymes production. Here, we used an Internal Transcribed Spacer 1 (ITS1) clone library to investigate the anaerobic rumen fungi in camel and to investigate their ability to produce cellulase and xylanase in vitro. Rumen fluid was collected from camels fed Egyptian clover (n = 14), and wheat straw (n = 7) and fecal samples were collected from camels fed wheat straw and concentrates (n = 5), or natural grazing plants (n = 10). Neocallimastix and Cyllamyces were the most abundant anaerobic fungi in all camel groups. An anaerobic rumen fungi media containing alfalfa hay as a carbon source was inoculated by rumen and fecal samples to assess the ability of anaerobic rumen fungi in camel gut to produce cellulase and xylanase. The anaerobic gut fungi in the camel is diverse and has cellulolytic and xylanolytic activities, fungal culture from rumen samples of camel fed wheat straw (R2) exhibited highest cellulase production. In addition, many of the sequences in the current study have no equivalent cultured representative, indicating a novel diversity within the camel gut.

Addressing Global Ruminant Agricultural Challenges Through Understanding the Rumen Microbiome: Past, Present, and Future

The rumen is a complex ecosystem composed of anaerobic bacteria, protozoa, fungi, methanogenic archaea and phages. These microbes interact closely to breakdown plant material that cannot be digested by humans, whilst providing metabolic energy to the host and, in the case of archaea, producing methane. Consequently, ruminants produce meat and milk, which are rich in high-quality protein, vitamins and minerals, and therefore contribute to food security. As the world population is predicted to reach approximately 9.7 billion by 2050, an increase in ruminant production to satisfy global protein demand is necessary, despite limited land availability, and whilst ensuring environmental impact is minimized. Although challenging, these goals can be met, but depend on our understanding of the rumen microbiome. Attempts to manipulate the rumen microbiome to benefit global agricultural challenges have been ongoing for decades with limited success, mostly due to the lack of a detailed understanding of this microbiome and our limited ability to culture most of these microbes outside the rumen. The potential to manipulate the rumen microbiome and meet global livestock challenges through animal breeding and introduction of dietary interventions during early life have recently emerged as promising new technologies. Our inability to phenotype ruminants in a high-throughput manner has also hampered progress, although the recent increase in “omic” data may allow further development of mathematical models and rumen microbial gene biomarkers as proxies. Advances in computational tools, high-throughput sequencing technologies and cultivation-independent “omics” approaches continue to revolutionize our understanding of the rumen microbiome. This will ultimately provide the knowledge framework needed to solve current and future ruminant livestock challenges.

1H NMR metabolomics of microbial metabolites in the four MW agricultural biogas plant reactors: A case study of inhibition mirroring the acute rumen acidosis symptoms

In this study, nuclear magnetic resonance (¹H NMR) spectroscopic profiling was used to provide a more comprehensive view of microbial metabolites associated with poor reactor performance in a full-scale 4 MW mesophilic agricultural biogas plant under fully operational and also under inhibited conditions. Multivariate analyses were used to assess the significance of differences between reactors whereas artificial neural networks (ANN) were used to identify the key metabolites responsible for inhibition and their network of interaction. Based on the results of nm-MDS ordination the subsamples of each reactor were similar, but not identical, despite homogenization of the full-scale reactors before sampling. Hence, a certain extent of variability due to the size of the system under analysis was transferred into metabolome analysis. Multivariate analysis showed that fully active reactors were clustered separately from those containing inhibited reactor metabolites and were significantly different. Furthermore, the three distinct inhibited states were significantly different from each other. The inhibited metabolomes were enriched in acetate, caprylate, trimethylamine, thymine, pyruvate, alanine, xanthine and succinate. The differences in the metabolic fingerprint between inactive and fully active reactors observed in this study resembled closely the metabolites differentiating the (sub) acute rumen acidosis inflicted and healthy rumen metabolomes, creating thus favorable conditions for the growth and activity of pathogenic bacteria. The consistency of our data with those reported before for rumen ecosystems shows that ¹H NMR based metabolomics is a reliable approach for the evaluation of metabolic events at full-scale biogas reactors.

Symposium review: Understanding diet-microbe interactions to enhance productivity of dairy cows

Ruminants are dependent on the microbiota (bacteria, protozoa, archaea, and fungi) that inhabit the reticulo-rumen for digestion of feedstuffs. Nearly 70% of energy and 50% of protein requirements for dairy cows are met by microbial fermentation in the rumen, emphasizing the need to characterize the role of microbes in feed breakdown and nutrient utilization. Over the past 2 decades, next-generation sequencing technologies have allowed for rapid expansion of knowledge concerning microbial populations and alterations in response to forages, concentrates, supplements, and probiotics in the rumen. Advances in gene sequencing and emerging bioinformatic tools have allowed for increased throughput of data to aid in our understanding of the functional relevance of microbial genomes. In particular, metagenomics can identify specific genes involved in metabolic pathways, and metatranscriptomics can describe the transcriptional activity of microbial genes. These powerful approaches help untangle the complex interactions between microbes and dietary nutrients so that we can more fully understand the physiology of feed digestion in the rumen. Application of genomics-based approaches offers promise in unraveling microbial niches and respective gene repertoires to potentiate fiber and nonfiber carbohydrate digestion, microbial protein synthesis, and healthy biohydrogenation. New information on microbial genomics and interactions with dietary components will more clearly define pathways in the rumen to positively influence milk yield and components.