Rumen microbial population dynamics in response to photoperiod

Spectres of Clock Evolution: Past, Present, and Yet to Come

Circadian clocks are phylogenetically widespread biological oscillators that allow organisms to entrain to environmental cycles and use their steady-state phase relationship to anticipate predictable daily phenomena – such as the light-dark transitions of a day – and prepare accordingly. Present from cyanobacteria to mammals, circadian clocks are evolutionarily ancient and are thought to increase the fitness of the organisms that possess them by allowing for better resource usage and/or proper internal temporal order. Here, we review literature with respect to the ecology and evolution of circadian clocks, with a special focus on cyanobacteria as model organisms. We first discuss what can be inferred about future clock evolution in response to climate change, based on data from latitudinal clines and domestication. We then address our current understanding of the role that circadian clocks might be contributing to the adaptive fitness of cyanobacteria at the present time. Lastly, we discuss what is currently known about the oldest known circadian clock, and the early Earth conditions that could have led to its evolution.

Characterisation of the effect of day length, and associated differences in dietary intake, on the gut microbiota of Soay sheep

Differences in the rumen bacterial community have been previously reported for Soay sheep housed under different day length conditions. This study extends this previous investigation to other organs of the digestive tract, as well as the analysis of ciliated protozoa and anaerobic fungi. The detectable concentrations of ciliated protozoa and anaerobic fungi decreased with increased day length in both the rumen and large colon, unlike those of bacteria where no effect was observed. Conversely, bacterial community composition was affected by day length in both the rumen and large colon, but the community composition of the detectable ciliated protozoa and anaerobic fungi was not affected. Day length-associated differences in the bacterial community composition extended to all of the organs examined, with the exception of the duodenum and the jejunum. It is proposed that differences in rumen fill and ruminal ‘by-pass’ nutrients together with endocrinological changes cause the observed effects of day length on the different gut microbial communities.

Multiple Vitamin K Forms Exist in Dairy Foods

Background: The plant-based form of vitamin K (phylloquinone, vitamin K-1) has been well quantified in the US diet. Menaquinones (vitamin K-2) are another class of vitamin K compounds that differ from phylloquinone in the length and saturation of their side chain, but they have not been well characterized in foods. Objectives: The objectives of this study were to 1) quantify phylloquinone and the different forms of menaquinones [menaquinone (MK) 4-MK13] in milk, yogurt, Greek yogurt, creams, and cheeses and 2) compare the menaquinone contents of full-fat, reduced-fat, and nonfat dairy products. Methods: All dairy samples were either obtained from the USDA National Food and Nutrient Analysis Program or purchased from retail outlets. Phylloquinone and menaquinone concentrations in these dairy products were quantified by mass spectrometry technology. Results: Full-fat dairy products contained appreciable amounts of menaquinones, primarily in the forms of MK9, MK10, and MK11. We also measured modest amounts of phylloquinone, MK4, MK8, and MK12 in these products. In contrast, there was little MK5-7 or MK13 detected in the majority of dairy products. The total vitamin K contents of soft cheese, blue cheese, semi-soft cheese, and hard cheese were (means ± SEMs): 506 ± 63, 440 ± 41, 289 ± 38, and 282 ± 5.0 µg/100 g, respectively. Nonfermented cheeses, such as processed cheese, contained lower amounts of vitamin K (98 ± 11 µg/100 g). Reduced-fat or fat-free dairy products contained ∼5-22% of the vitamin K found in full-fat equivalents. For example, total vitamin K contents of full-fat milk (4% fat), 2%-fat milk, 1%-fat milk, and nonfat milk were 38.1 ± 8.6, 19.4 ± 7.7, 12.9 ± 2.0, and 7.7 ± 2.9 µg/100 g, respectively. Conclusions: To the best of our knowledge, this is the first report of menaquinone contents of US dairy products. Findings indicate that the amount of vitamin K contents in dairy products is high and proportional to the fat content of the product.

Seasonal changes in the digesta-adherent rumen bacterial communities of dairy cattle grazing pasture

The complex microbiota that resides within the rumen is responsible for the break-down of plant fibre. The bacteria that attach to ingested plant matter within the rumen are thought to be responsible for initial fibre degradation. Most studies examining the ecology of this important microbiome only offer a ‘snapshot’ in time. We monitored the diversity of rumen bacteria in four New Zealand dairy cows, grazing a rye-grass and clover pasture over five consecutive seasons, using high throughput pyrosequencing of bacterial 16S rRNA genes. We chose to focus on the digesta-adherent bacterial community to learn more about the stability of this community over time. 16S rRNA gene sequencing showed a high level of bacterial diversity, totalling 1539 operational taxonomic units (OTUs, grouped at 96% sequence similarity) across all samples, and ranging from 653 to 926 OTUs per individual sample. The nutritive composition of the pasture changed with the seasons as did the production phase of the animals. Sequence analysis showed that, overall, the bacterial communities were broadly similar between the individual animals. The adherent bacterial community was strongly dominated by members of Firmicutes (82.1%), followed by Bacteroidetes (11.8%). This community differed between the seasons, returning to close to that observed in the same season one year later. These seasonal differences were only small, but were statistically significant (p < 0.001), and were probably due to the seasonal differences in the diet. These results demonstrate a general invariability of the ruminal bacterial community structure in these grazing dairy cattle.

Methods for taxonomic studies of rumen ciliates (alveolata: ciliophora): a brief review

This review presents the principal methods used in taxonomic studies of rumen ciliates: live observation, Lugol staining, fixation and staining with methyl-green formalin saline (MFS) solution, protargol staining, silver carbonate impregnation, scanning electron microscopy and molecular techniques. Mastering these techniques is essential for successful research on the taxonomy of rumen ciliates. No single technique reveals all of the characteristics required for a complete description of a rumen ciliate; therefore, it is necessary to combine the use of these techniques as appropriate to the rumen ciliate group under study. Tables are provided to summarize: 1) morphological methods more appropriate for revealing morphological structures of interest, 2) morphological methods indicated for each group of rumen ciliates, and 3) main primers used for PCR amplification of the 18S rDNA of rumen ciliates.

The Role of Ciliate Protozoa in the Rumen

First described in 1843, Rumen protozoa with their striking appearance were assumed to be important for the welfare of their host. However, despite contributing up to 50% of the bio-mass in the rumen, the role of protozoa in rumen microbial ecosystem remains unclear. Phylogenetic analysis of 18S rDNA libraries generated from the rumen of cattle, sheep, and goats has revealed an unexpected diversity of ciliated protozoa although variation in gene copy number between species makes it difficult to obtain absolute quantification. Despite repeated attempts it has proven impossible to maintain rumen protozoa in axenic culture. Thus it has been difficult to establish conclusively a role of ciliate protozoa in rumen fiber degradation. The development of techniques to clone and express ciliate genes in λ phage, together with bioinformatic indices to confirm the ciliate origin of the genes has allowed the isolation and characterization of fibrolytic genes from rumen protozoa. Elimination of the ciliate protozoa increases microbial protein supply by up to 30% and reduces methane production by up to 11%. Our recent findings suggest that holotrich protozoa play a disproportionate role in supporting methanogenesis whilst the small Entodinium are responsible for much of the bacterial protein turnover. As yet no method to control protozoa in the rumen that is safe and practically applicable has been developed, however a range of plant extract capable of controlling if not completely eliminating rumen protozoa have been described.

Animal-microbial symbioses in changing environments

The environments in which animals have evolved and live have profound effects on all aspects of their biology. Predictable rhythmic changes in the physical environment are arguably among the most important forces shaping the evolution of behavior and physiology of animals, and to anticipate and prepare for these predictable changes, animals have evolved biological clocks. Unpredictable changes in the physical environment have important impacts on animal biology as well. The ability of animals to cope with and survive unpredictable perturbations depends on phenotypic plasticity and/or microevolution. From the time metazoans first evolved from their protistan ancestors they have lived in close association with a diverse array of microbes that have influenced, in some way, all aspects of the evolution of animal structure, function and behavior. Yet, few studies have addressed whether daily or seasonal rhythms may affect, or be affected by, an animal's microbial symbionts. This survey highlights how biologists interested in the ecological and evolutionary physiology of animals whose lifestyles are influenced by environmental cycles may benefit from considering whether symbiotic microbes have shaped the features they study.

Intact brown seaweed (Ascophyllum nodosum) in diets of weaned piglets: effects on performance, gut bacteria and morphology and plasma oxidative status

The aim was to assess the effects of intact dried Ascophyllum nodosum seaweed on piglet performances, gut bacteria and function and plasma oxidative status. A total of 160 weaned piglets (21 days, 6.59 ± 0.91 kg) were allocated to four dietary treatments with eight pen replicates of five animals each for 28 days: a control diet; based on cereals, soybean meal and milk products, and three basal diets supplemented with either 2.5, 5.0 or 10.0 g dried seaweed per kg. At day 12/13 one piglet from each pen was sacrificed. Plasma samples were taken to determine parameters of oxidative status. Digesta were sampled for microbiological plate countings onto selective media and molecular analysis using PCR-DGGE. Small intestinal tissue was taken for morphological and electro-physiological determinations. Data were analysed by a linear model with treatment as fixed effect. A. nodosum supplementation had no effect on daily weight gain, nor did it alter feed conversion ratio. Plate countings failed to reveal differences among treatments. Dendograms prepared using PCR-DGGE banding patterns did not indicate clustering of microbial profiles based on diet supplement. Plasma oxidative status and outcome of morphology and of electro-physiological measurements from gut tissues were similar for all treatments. Thus, the addition of A. nodosum seaweed to well digestible diets did not enhance performances of piglets nor some gut health parameters and plasma oxidative status.

Biodiversity and fermentative activity of caecal microbial communities in wild and farm rabbits from Spain

In order to study the microbial caecal ecosystem of wild and domestic rabbits through the fermentation characteristics and concentration and diversity of bacterial and archaeal communities, caecal samples from sixteen wild rabbits (WR) were contrasted with two groups (n = 4) of farm rabbits receiving low (LSF) or high (HSF) soluble fibre diets from 28 (weaning) to 51 days of age. DNA was extracted for quantifying bacteria and Archaea by qPCR and for biodiversity analysis of microbial communities by DGGE. Samples from WR had lower caecal pH and ammonia and higher volatile fatty acids concentration than farm animals. Lower acetate and higher butyrate proportions were detected in WR. Bacterial and archaeal DGGE profiles were clearly different between wild and farm rabbits, and diet-affected population of farm rabbits. Similarity index of bacteria was lower than 0.40 among WR, and 0.52 among farm rabbits. In conclusion, caecal fermentation characteristics differ between wild and farm rabbits, which harbour clearly different bacterial and archaeal communities. In farm rabbits, diversity is influenced by the dietary level of soluble fibre.

Populations of select cultured and uncultured bacteria in the rumen of sheep and the effect of diets and ruminal fractions

The objective of this study was to assess the importance of select cultured and uncultured bacteria in the rumen by quantifying their populations and the effect of diets and ruminal fractions. Full-length 16S rRNA gene (rrs) sequences were recovered from rumen samples using specific primers designed from partial sequences recovered previously. Five uncultured bacterial operational taxonomic units (OTUs) were quantified using specific quantitative PCR (qPCR) in fractionated ruminal samples from sheep fed either hay alone or hay plus corn. Species Fibrobacter succinogenes, Ruminococcus albus, R. flavefaciens, Ruminobacter amylophilus, Selenomonas ruminantium, and Mitsuokella multacida and genera Butyrivibrio and Prevotella were also quantified as comparison. The full-length rrs sequence improved taxonomic assignments of partial rrs sequences. Genus Prevotella had the greatest abundance. Of the three major cultured cellulolytic species, R. flavefaciens was most abundant, followed by R. albus and F. succinogenes. The five uncultured bacterial OTUs, classified to genus Acetivibrio, genus Allobaculum, family Ruminococcaceae, order Clostridiales, or class Clostridia, had abundance comparable to that of the above species of genera except Prevotella. Corn supplementation and fractions affected distribution of the rumen bacteria, but to a limited extent. When compared to the qPCR data, sequence frequencies in the rrs clone libraries tended to overestimate the abundance of the bacteria represented. This study showed that abundance and population dynamics of uncultured bacteria can be quantified by specific qPCR, which complements the results of rrs clone libraries. This study also revealed that some uncultured bacteria might be as important as some of the well-characterized bacteria in the rumen. The approach used should be applicable to assess the abundance and potential importance of uncultured bacteria in other environments.

Correlation of particular bacterial PCR-denaturing gradient gel electrophoresis patterns with bovine ruminal fermentation parameters and feed efficiency traits

The influence of rumen microbial structure and functions on host physiology remains poorly understood. This study aimed to investigate the interaction between the ruminal microflora and the host by correlating bacterial diversity with fermentation measurements and feed efficiency traits, including dry matter intake, feed conversion ratio, average daily gain, and residual feed intake, using culture-independent methods. Universal bacterial partial 16S rRNA gene products were amplified from ruminal fluid collected from 58 steers raised under a low-energy diet and were subjected to PCR-denaturing gradient gel electrophoresis (DGGE) analysis. Multivariate statistical analysis was used to relate specific PCR-DGGE bands to various feed efficiency traits and metabolites. Analysis of volatile fatty acid profiles showed that butyrate was positively correlated with daily dry matter intake (P < 0.05) and tended to have higher concentration in inefficient animals (P = 0.10), while isovalerate was associated with residual feed intake (P < 0.05). Our results suggest that particular bacteria and their metabolism in the rumen may contribute to differences in host feed efficiency under a low-energy diet. This is the first study correlating PCR-DGGE bands representing specific bacteria to metabolites in the bovine rumen and to host feed efficiency traits.

Photoperiod modulates gut bacteria composition in male Siberian hamsters (Phodopus sungorus)

Seasonal changes in day length (i.e., photoperiod) provide animals with a reliable environmental cue to determine time of year, and many physiological changes occur in laboratory animals simply by extending or shortening day length. Male Siberian hamsters (Phodopus sungorus) housed in long summer-like day lengths have significantly elevated body and fat masses compared to short-day hamsters. Because others have demonstrated that the intestinal microbiota of humans and rodents promotes host adiposity, we hypothesized that photoperiod-induced changes in body and fat masses could be associated with changes in the microbial composition in the intestines. We used bacterial tag-encoded FLX amplicon pyrosequencing (bTEFAP) to assess microbial diversity in the cecal contents of hamsters; long days significantly increased the relative abundance of bacteria in the phylum Proteobacteria. This effect was primarily due to a significant increase in the abundance of the genus Citrobacter, with both the abundance of Proteobacteria and Citrobacter spp. significantly correlated with body mass and with inguinal fat mass. In general, the abundance of the Firmicutes phylum was inversely associated with body mass. These data indicate that the intestinal microbiota are responsive to changes in photoperiod and suggest that these changes may in part influence photoperiodic changes in body and fat masses.

Changes in the bacterial population of the caecum and stomach of the rabbit in response to addition of dietary caprylic acid

The effect of caprylic acid, either in its pure form, or as Akomed R, on the microbial community of the stomach and caecum of farmed rabbits was investigated. This fatty acid, which is often added to the diet of farmed rabbits to reduce mortality rates was shown to reduce the number of coliforms isolated from both the stomach and the caecum. Moreover, it led to a reduction in the total number of anaerobic bacteria isolated from the caecum, but not for those isolated from the stomach. Its mode of action remains unclear, but here it is shown by use of both DGGE and TRFLP analysis that these changes are not confined to one specific group of bacteria, but rather affects a number of species.

Comparative studies of microbial populations in the rumen, duodenum, ileum and faeces of lactating dairy cows

AIMS

Understanding factors that influence the composition of microbial populations of the digestive system of dairy cattle will be key in regulating these populations to improve animal performance. Although rumen microbes are well studied, little is known of the dynamics and role of microbial populations in the small intestine of cows. Comparisons of fingerprints of microbial populations were used to investigate the effects of gastrointestinal (GI) segment and animal on community structure.

METHODS AND RESULTS

Samples from four lactating dairy cows with ruminal, duodenal and ileal cannulae were collected. Terminal-restriction fragment length polymorphism (T-RFLP) comparisons of small subunit rRNA genes revealed differences in microbial populations between GI segments (P < 0.05). No significant differences in either methanogen populations or microbial community profiles between animals were observed. Quantitative PCR was used to assay relative changes in methanogen numbers compared to procaryote rRNA gene numbers, and direct microscopic counts were used to enumerate total procaryote numbers of the duodenal and ileal samples.

CONCLUSIONS

T-RFLP comparisons illustrate significant changes in microbial diversity as digesta passes from one segment to another. Direct counts indicate that microbial numbers are reduced by eight orders of magnitude from the rumen, through the abomasum, and into the duodenum (from c. 10(12) to c. 3.6 x 10(4) cells per ml). Quantitative PCR analyses of rRNA genes indicate that methanogens are present in the duodenum and ileum.

SIGNIFICANCE AND IMPACT OF THE STUDY

The contribution of microbial populations of the small intestine to the nutrition and health of cattle is seldom addressed but warrants further investigation.

Linkage of microbial ecology to phenotype: correlation of rumen microbial ecology to cattle's feed efficiency

Linkage of rumen microbial structure to host phenotypical traits may enhance the understanding of host-microbial interactions in livestock species. This study used culture-independent PCR-denaturing gradient gel electrophoresis (PCR-DGGE) to investigate the microbial profiles in the rumen of cattle differing in feed efficiency. The analysis of detectable bacterial PCR-DGGE profiles showed that the profiles generated from efficient steers clustered together and were clearly separated from those obtained from inefficient steers, indicating that specific bacterial groups may only inhabit in efficient steers. In addition, the bacterial profiles were more likely clustered within a certain breed, suggesting that host genetics may play an important role in rumen microbial structure. The correlations between the concentrations of volatile fatty acids and feed efficiency traits were also observed. Significantly higher concentrations of butyrate (P < 0.001) and valerate (P = 0.006) were detected in the efficient steers. Our results revealed potential associations between the detectable rumen microbiota and its fermentation parameters with the feed efficiency of cattle.

Evaluations of different hypervariable regions of archaeal 16S rRNA genes in profiling of methanogens by Archaea-specific PCR and denaturing gradient gel electrophoresis

Different hypervariable (V) regions of the archaeal 16S rRNA gene (rrs) were compared systematically to establish a preferred V region(s) for use in Archaea-specific PCR-denaturing gradient gel electrophoresis (DGGE). The PCR products of the V3 region produced the most informative DGGE profiles and permitted identification of common methanogens from rumen samples from sheep. This study also showed that different methanogens might be detected when different V regions are targeted by PCR-DGGE. Dietary fat appeared to transiently stimulate Methanosphaera stadtmanae but inhibit Methanobrevibacter sp. strain AbM4 in rumen samples.

The host species affects the microbial community in the goat rumen

AIMS

This study was carried out to determine whether bacterial and ciliate populations in goat rumen vary significantly between different goat species living in the same environment.

METHODS AND RESULTS

Bacterial and ciliate communities in the rumen of three goat species were analysed at the molecular level using denaturing gradient gel electrophoresis. The microbial community varied considerably among goats living in the same environment. Interspecies variation in the bacterial population was noticeably greater than intraspecies variation. In contrast, there was considerable variation in the ciliate population among goats within the same species, and intraspecies similarities were no greater than those observed across species.

CONCLUSIONS

Because environmental factors and diets were identical for all goats, differences in bacterial populations reflect species-specific differences in rumen microbes.

SIGNIFICANCE AND IMPACT OF THE STUDY

Factors related to the host species have an important effect on determining the bacterial composition in the goat rumen.

The effect of medicated diets and level of feeding on caecal microbiota of lactating rabbit does

AIMS

To study the effect of the type of antibiotic used in medicated diets against pathogens and the feeding level on the microbial biodiversity in the rabbit caecum.

METHODS AND RESULTS

Three groups of eight does were given a diet unsupplemented (NAB) or with 100 ppm of bacitracin (BAC) or tiamulin (TIA). Litter sizes of four does in each group were adjusted to five (LS5) or to nine (LS9), to manipulate their levels of feed intake. The feeding level strongly affected caecal microbiota in does fed on NAB and BAC diet, whereas the effect of the antibiotic was higher in TIA-supplemented animals, even prevailing over the effect of feeding level. Daily food intake and milk yield (P<0.05) and caecum weight (P<0.10) were higher in feeding of LS9 does. The total volatile fatty acid concentration was lower with BAC (P<0.05).

CONCLUSIONS

The feeding level strongly affects caecal biodiversity in lactating does. The extent of the antibiotic effect depends on its nature, being significant with TIA but not with BAC.

SIGNIFICANCE AND IMPACT OF THE STUDY

Changes in the feeding level promote different profiles of caecal microbiota. Therapeutic doses of TIA may affect caecal microbiota, whereas BAC would not reduce diversity.

The effect of lactating rabbit does on the development of the caecal microbial community in the pups they nurture

AIMS

To study the effect of microbial community of the rabbit does as influenced by dietary factors, on the development of the gut microbiota of their litters.

METHODS AND RESULTS

Twenty-four lactating does were given a diet unsupplemented (NAB) or with 100 ppm of bacitracin (BAC) or tiamulin (TIA) to modify their digestive microbiota. Litters were adjusted to six pups. In Trial 1, four does per diet milked their own six pups. In Trial 2, two does per diet nursed three of their pups and three fostered from the doe given the same diet. In Trial 3, two does on each diet nursed three of their pups and three fostered from another doe fed on another diet. Denaturing gradient gel electrophoresis (DGGE) analyses of the litter microbiota showed that the effect of the milking mother was greater than the influence of the biological mother. TIA had a strong effect on the bacterial profile even prevailing over that of the milking mother, in contrast to BAC.

CONCLUSIONS

Nursing mother microbiota plays an important role over that of the litter. Caecal colonization that occurs during the lactation process prevailed over that during the partum.

SIGNIFICANCE AND IMPACT OF THE STUDY

Manipulation of the mother's microbiota may help for adaptation of the litter microbial community against pathologic digestive processes.

Effect of antibiotics on the bacterial population of the rabbit caecum

The effect feeding antibiotics has on the bacterial population of the rabbit caecum was investigated. No changes in total volatile fatty acid production or total bacterial counts were observed compared with nonantibiotic treated controls. However, treatment with chlortetracycline resulted in an increase of propionate at the apparent cost of butyrate (P<0.05). Denaturing gradient gel electrophoresis analysis indicated that the two antibiotics that inhibit protein synthesis (chlortetracycline and tiamulin) exerted the most similar changes on the bacterial population structure, decreasing the diversity of the profiles. Sequence analysis of DNA from excised denaturing gradient gel electrophoresis bands was carried out. The majority of the sequences observed were most similar to bacterial sequences previously described in other gut environments, with 11% being most similar to those previously reported from the rabbit, and 95% of the sequences having 95% or greater identity to sequences already in GenBank.