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1.  Methane Emission by Camelids 
PLoS ONE  2014;9(4):e94363.
Methane emissions from ruminant livestock have been intensively studied in order to reduce contribution to the greenhouse effect. Ruminants were found to produce more enteric methane than other mammalian herbivores. As camelids share some features of their digestive anatomy and physiology with ruminants, it has been proposed that they produce similar amounts of methane per unit of body mass. This is of special relevance for countrywide greenhouse gas budgets of countries that harbor large populations of camelids like Australia. However, hardly any quantitative methane emission measurements have been performed in camelids. In order to fill this gap, we carried out respiration chamber measurements with three camelid species (Vicugna pacos, Lama glama, Camelus bactrianus; n = 16 in total), all kept on a diet consisting of food produced from alfalfa only. The camelids produced less methane expressed on the basis of body mass (0.32±0.11 L kg−1 d−1) when compared to literature data on domestic ruminants fed on roughage diets (0.58±0.16 L kg−1 d−1). However, there was no significant difference between the two suborders when methane emission was expressed on the basis of digestible neutral detergent fiber intake (92.7±33.9 L kg−1 in camelids vs. 86.2±12.1 L kg−1 in ruminants). This implies that the pathways of methanogenesis forming part of the microbial digestion of fiber in the foregut are similar between the groups, and that the lower methane emission of camelids can be explained by their generally lower relative food intake. Our results suggest that the methane emission of Australia's feral camels corresponds only to 1 to 2% of the methane amount produced by the countries' domestic ruminants and that calculations of greenhouse gas budgets of countries with large camelid populations based on equations developed for ruminants are generally overestimating the actual levels.
doi:10.1371/journal.pone.0094363
PMCID: PMC3981797  PMID: 24718604
2.  The life cycle of Trypanosoma (Nannomonas) congolense in the tsetse fly 
Parasites & Vectors  2012;5:109.
Background
The tsetse-transmitted African trypanosomes cause diseases of importance to the health of both humans and livestock. The life cycles of these trypanosomes in the fly were described in the last century, but comparatively few details are available for Trypanosoma (Nannomonas) congolense, despite the fact that it is probably the most prevalent and widespread pathogenic species for livestock in tropical Africa. When the fly takes up bloodstream form trypanosomes, the initial establishment of midgut infection and invasion of the proventriculus is much the same in T. congolense and T. brucei. However, the developmental pathways subsequently diverge, with production of infective metacyclics in the proboscis for T. congolense and in the salivary glands for T. brucei. Whereas events during migration from the proventriculus are understood for T. brucei, knowledge of the corresponding developmental pathway in T. congolense is rudimentary. The recent publication of the genome sequence makes it timely to re-investigate the life cycle of T. congolense.
Methods
Experimental tsetse flies were fed an initial bloodmeal containing T. congolense strain 1/148 and dissected 2 to 78 days later. Trypanosomes recovered from the midgut, proventriculus, proboscis and cibarium were fixed and stained for digital image analysis. Trypanosomes contained in spit samples from individually caged flies were analysed similarly. Mensural data from individual trypanosomes were subjected to principal components analysis.
Results
Flies were more susceptible to infection with T. congolense than T. brucei; a high proportion of flies infected with T. congolense established a midgut and subsequent proboscis infection, whereas many T. brucei infections were lost in the migration from foregut to salivary glands. In T. congolense, trypomastigotes ceased division in the proventriculus and became uniform in size. The trypanosomes retained trypomastigote morphology during migration via the foregut to the mouthparts and we confirmed that the trypomastigote-epimastigote transition occurred in the proboscis. We found no equivalent to the asymmetric division stage in T. brucei that mediates transition of proventricular trypomastigotes to epimastigotes. In T. congolense extremely long epimastigotes with remarkably elongated posterior ends were observed in both the proboscis and cibarium; no difference was found in the developmental stages in these two organs. Dividing trypomastigotes and epimastigotes were recovered from the proboscis, some of which were in transition from trypomastigote to epimastigote and vice versa. It remains uncertain whether these morphological transitions are mediated by cell division, since we also found non-dividing cells with a variously positioned, juxta-nuclear kinetoplast.
Conclusions
We have presented a detailed description of the life cycle of T. congolense in its tsetse fly vector. During development in the fly T. congolense shares a common migratory pathway with its close relative T. brucei, culminating in the production of small metacyclic trypanosomes that can be inoculated with the saliva. Despite this outward similarity in life cycle, the transitional developmental stages in the foregut and mouthparts are remarkably different in the two trypanosome species.
doi:10.1186/1756-3305-5-109
PMCID: PMC3384477  PMID: 22676292
3.  Characterization of the bovine type I IFN locus: rearrangements, expansions, and novel subfamilies 
BMC Genomics  2009;10:187.
Background
The Type I interferons (IFN) have major roles in the innate immune response to viruses, a function that is believed to have led to expansion in the number and complexity of their genes, although these genes have remained confined to single chromosomal region in all mammals so far examined. IFNB and IFNE define the limits of the locus, with all other Type I IFN genes except IFNK distributed between these boundaries, strongly suggesting that the locus has broadened as IFN genes duplicated and then evolved into a series of distinct families.
Results
The Type I IFN locus in Bos taurus has undergone significant rearrangement and expansion compared to mouse and human, however, with the constituent genes separated into two sub-loci separated by >700 kb. The IFNW family is greatly expanded, comprising 24 potentially functional genes and at least 8 pseudogenes. The IFNB (n = 6), represented in human and mouse by one copy, are also present as multiple copies in Bos taurus. The IFNT, which encode a non-virally inducible, ruminant-specific IFN secreted by the pre-implantation conceptus, are represented by three genes and two pseudogenes. The latter have sequences intermediate between IFNT and IFNW. A new Type I IFN family (IFNX) of four members, one of which is a pseudogene, appears to have diverged from the IFNA lineage at least 83 million years ago, but is absent in all other sequenced genomes with the possible exception of the horse, a non-ruminant herbivore.
Conclusion
In summary, we have provided the first comprehensive annotation of the Type I IFN locus in Bos taurus, thereby providing an insight into the functional evolution of the Type I IFN in ruminants. The diversity and global spread of the ruminant species may have required an expansion of the Type I IFN locus and its constituent genes to provide broad anti-viral protection required for foraging and foregut fermentation.
doi:10.1186/1471-2164-10-187
PMCID: PMC2680415  PMID: 19393062
4.  Comparative analyses of foregut and hindgut bacterial communities in hoatzins and cows 
The ISME Journal  2011;6(3):531-541.
Foregut fermentation occurs in mammalian ruminants and in one bird, the South American folivorous hoatzin. This bird has an enlarged crop with a function analogous to the rumen, where foregut microbes degrade the otherwise indigestible plant matter, providing energy to the host from foregut fermentation, in addition to the fermentation that occurs in their hindguts (cecum/colon). As foregut fermentation represents an evolutionary convergence between hoatzins and ruminants, our aim was to compare the community structure of foregut and hindgut bacterial communities in the cow and hoatzin to evaluate the influences of host phylogeny and organ function in shaping the gut microbiome. The approach used was to hybridize amplified bacterial ribosomal RNA genes onto a high-density microarray (PhyloChip). The results show that the microbial communities cluster primarily by functional environment (foreguts cluster separately from hindguts) and then by host. Bacterial community diversity was higher in the cow than in the hoatzin. Overall, compared with hindguts, foreguts have higher proportions of Bacteroidetes and Spirochaetes, and lower proportions of Firmicutes and Proteobacteria. The main host differences in gut bacterial composition include a higher representation of Spirochaetes, Synergistetes and Verrucomicrobia in the cow. Despite the significant differences in host phylogeny, body size, physiology and diet, the function seems to shape the microbial communities involved in fermentation. Regardless of the independent origin of foregut fermentation in birds and mammals, organ function has led to convergence of the microbial community structure in phylogenetically distant hosts.
doi:10.1038/ismej.2011.131
PMCID: PMC3280141  PMID: 21938024
microbiota; foregut; hindgut; hoatzin; cow; PhyloChip
5.  Accessing Local Knowledge to Identify Where Species of Conservation Concern Occur in a Tropical Forest Landscape 
Environmental Management  2013;52(2):348-359.
Conventional biodiversity surveys play an important role in ensuring good conservation friendly management in tropical forest regions but are demanding in terms of expertise, time, and budget. Can local people help? Here, we illustrate how local knowledge can support low cost conservation surveys. We worked in the Malinau watershed, East Kalimantan, Indonesia, an area currently at risk of extensive forest loss. We selected eight species of regional conservation interest: rafflesia (Rafflesia spp.), black orchid (Coelogyne pandurata), sun bear (Helarctos malayanus), tarsier (Tarsius bancanus), slow loris (Nycticebus coucang), proboscis monkey (Nasalis larvatus), clouded leopard (Neofelis diardi/N. nebulosa), and orang-utan (Pongo pygmaeus). We asked 52 informants in seven villages if, where and when they had observed these species. We used maps, based on both geo-referenced and sketched features, to record these observations. Verification concerns and related issues are discussed. Evaluations suggest our local information is reliable. Our study took 6 weeks and cost about USD 5000. Extensive expert based field surveys across the same region would cost one or two orders of magnitude more. The records extend the known distribution for sun bear, tarsier, slow loris, and clouded leopard. Reports of rafflesia, proboscis monkey, and orang-utan are of immediate conservation significance. While quality concerns should never be abandoned, we conclude that local people can help expand our knowledge of large areas in an effective, reliable, and low cost manner and thus contribute to improved management.
doi:10.1007/s00267-013-0051-7
PMCID: PMC3713271  PMID: 23633002
Local knowledge; Accuracy; Expertise time and budget; Conservation; East Kalimantan
6.  Sex-Age Related Rumination Behavior of Père David’s Deer under Constraints of Feeding Habitat and Rainfall 
PLoS ONE  2013;8(6):e66261.
Extensive studies have been conducted on the rumination behavior of domestic herbivores. However, studies on wild animals are limited, particularly wild animals with specific ruminating parameters. In this study, Père David’s deer, a previously extirpated species, was observed to analyze the effects of sex-age, feeding habitat, and rainfall on rumination behavior in the Dafeng Nature Reserve, China. Rumination behavior was investigated based on four parameters: proportion of bedding time spent chewing, bolus processing time (s/bolus), chewing frequency (chews/bolus), and chewing rate (chews/s). Results showed that all three factors affect rumination behavior. The extent of their effects varied based on the four rumination parameters. Chewing rate and frequency decreased based on sex–age levels, i.e., from fawns to juvenile female, juvenile male, adult female, stag, and harem holder. Therefore, body size played a major role in shaping rumination behavior. Deer found in grasslands could chew faster compared with deer found in woodlands. This result might be caused by the effects of dietary composition and sunlight intensity. A deer spends a longer time ruminating while bedding during rainy days compared with rainless days to maximize energy and nutrition intake and compensate for the loss of feeding time during rainy days. Therefore, rumination behavior is plastic and is shaped by intrinsic and extrinsic factors.
doi:10.1371/journal.pone.0066261
PMCID: PMC3688877  PMID: 23823072
7.  Barx1-Mediated Inhibition of Wnt Signaling in the Mouse Thoracic Foregut Controls Tracheo-Esophageal Septation and Epithelial Differentiation 
PLoS ONE  2011;6(7):e22493.
Mesenchymal cells underlying the definitive endoderm in vertebrate animals play a vital role in digestive and respiratory organogenesis. Although several signaling pathways are implicated in foregut patterning and morphogenesis, and despite the clinical importance of congenital tracheal and esophageal malformations in humans, understanding of molecular mechanisms that allow a single tube to separate correctly into the trachea and esophagus is incomplete. The homoebox gene Barx1 is highly expressed in prospective stomach mesenchyme and required to specify this organ. We observed lower Barx1 expression extending contiguously from the proximal stomach domain, along the dorsal anterior foregut mesenchyme and in mesenchymal cells between the nascent esophagus and trachea. This expression pattern exactly mirrors the decline in Wnt signaling activity in late development of the adjacent dorsal foregut endoderm and medial mainstem bronchi. The hypopharynx in Barx1−/− mouse embryos is abnormally elongated and the point of esophago-tracheal separation shows marked caudal displacement, resulting in a common foregut tube that is similar to human congenital tracheo-esophageal fistula and explains neonatal lethality. Moreover, the Barx1−/− esophagus displays molecular and cytologic features of respiratory endoderm, phenocopying abnormalities observed in mouse embryos with activated ß-catenin. The zone of canonical Wnt signaling is abnormally prolonged and expanded in the proximal Barx1−/− foregut. Thus, as in the developing stomach, but distinct from the spleen, Barx1 control of thoracic foregut specification and tracheo-esophageal septation is tightly associated with down-regulation of adjacent Wnt pathway activity.
doi:10.1371/journal.pone.0022493
PMCID: PMC3142160  PMID: 21799872
8.  The diversity of the fecal bacterial community and its relationship with the concentration of volatile fatty acids in the feces during subacute rumen acidosis in dairy cows 
Background
Sub-acute ruminal acidosis (SARA) is a well-recognized digestive disorder found in particular in well-managed dairy herds. SARA can result in increased flow of fermentable substrates to the hindgut, which can increase the production of volatile fatty acids, alter the structure of the microbial community, and have a negative effect on animal health and productivity. However, little is known about changes in the structure of the microbial community and its relationship with fatty acids during SARA. Four cannulated primiparous (60 to 90 day in milk) Holstein dairy cows were assigned to two diets in a 2 × 2 crossover experimental design. The diets contained (on a dry matter basis): 40% (control diet, COD) and 70% (SARA induction diet, SAID) concentrate feeds. Samples of ruminal fluid and feces were collected on day 12, 15, 17 and 21 of the treatment period, and the pH was measured in the ruminal and fecal samples; the fecal microbiota was determined by pyrosequencing analysis of the V1–V3 region of amplified 16S ribosomal RNA (16S rRNA).
Results
SAID decreased ruminal and fecal pH and increased the propionate, butyrate and total volatile fatty acid (TVFA) concentration in feces when compared with the COD. A barcoded DNA pyrosequencing method was used to generate 2116 16S operational taxonomic units (OTUs). A total of 11 phyla were observed, distributed amongst all cattle on both diets; however, only 5 phyla were observed in all animals regardless of dietary treatment, and considerable animal to animal variation was revealed. The average abundance and its range of the 5 phyla were as follows: Firmicutes (63.7%, 29.1–84.1%), Proteobacteria (18.3%, 3.4–46.9%), Actinobacteria (6.8%, 0.4–39.9%), Bacteroidetes (7.6%, 2.2–17.7%) and Tenericutes (1.6%, 0.3–3%). Feeding the SAID resulted in significant shifts in the structure of the fecal microbial community when compared with the traditional COD. Among the 2116 OTUs detected in the present study, 88 OTUs were affected significantly by diet; and the proportion of these OTUs was 20.6% and 17.4% among the total number of sequences, respectively. Among the OTUs affected, the predominant species, including OTU2140 (G: Turicibacter), OTU1695 (G: Stenotrophomonas) and OTU8143 (F: Lachnospiraceae), were increased, while the abundance of OTU1266 (S: Solibacillus silvestris) and OTU2022 (G: Lysinibacillus) was reduced in the SAID group compared with the COD. Further, our results indicated that the fecal volatile fatty acid (VFA) concentrations were significantly related to presence of some certain species of Bacteroidetes and Firmicutes in the feces.
Conclusions
This is, to our knowledge, the first study that has used barcoded DNA pyrosequencing to survey the fecal microbiome of dairy cattle during SARA. Our results suggest that particular bacteria and their metabolites in the feces appear to contribute to differences in host health between those given SAID and traditional COD feeding. A better understanding of these microbial populations will allow for improved nutrient management and increased animal growth performance.
doi:10.1186/1746-6148-8-237
PMCID: PMC3582618  PMID: 23217205
Subacute rumen acidosis; Fecal bacterial community; Volatile fatty acid; Dairy cows
9.  Eating Time Modulations of Physiology and Health: Life Lessons from Human and Ruminant Models 
Tissue nutrient supply may be synchronized with endogenous physiological rhythms to optimize animal and human health. Glucose tolerance and insulin sensitivity have endogenous rhythms that are not essentially dependent on food type and eating. Human glucose tolerance declines as day comes into night. Based on such evolutionary findings, large evening meals must be avoided to reduce risks of visceral adiposity, diabetes, hypertension and related cardiovascular complexities. Ruminants as extremely important food-producing livestock have evolved to ruminate mostly overnight when little grazing occurs, and when rumen reaches a larger volume and fermentation capacity. As such, eating time (e.g., evening vs. morning) will alter postprandial and diurnal patterns of food intake, rumen and peripheral metabolites production and supply, and milk and meat production efficiency. Most recent discoveries suggest that eating time modulates postprandial intake and metabolism patterns in non-grazing lactating cows. Eating rate and absolute intake can increase by evening vs. morning feeding in dairy cows. Evening feeding increased postprandial rumen volatile fatty acids (VFA) peak, and surges of blood insulin, lactate and beta-hydroxybutyrate, and induced a peripartal decline in blood glucose. As a result, milk fat and energy production were increased. While being unfavorable to human health, evening and night feeding have proved beneficial to ruminants. These findings establish a differential chronological basis for food intake and nutrient metabolism in man and food-producing animals. Eating time is a major external cue and a feasible life strategy that affects production and health physiology.
PMCID: PMC3586911  PMID: 23492863
Eating time; Health; Human; Physiology; Ruminant
10.  Activity-Based Metagenomic Screening and Biochemical Characterization of Bovine Ruminal Protozoan Glycoside Hydrolases▿† 
Applied and Environmental Microbiology  2011;77(22):8106-8113.
The rumen, the foregut of herbivorous ruminant animals such as cattle, functions as a bioreactor to process complex plant material. Among the numerous and diverse microbes involved in ruminal digestion are the ruminal protozoans, which are single-celled, ciliated eukaryotic organisms. An activity-based screen was executed to identify genes encoding fibrolytic enzymes present in the metatranscriptome of a bovine ruminal protozoan-enriched cDNA expression library. Of the four novel genes identified, two were characterized in biochemical assays. Our results provide evidence for the effective use of functional metagenomics to retrieve novel enzymes from microbial populations that cannot be maintained in axenic cultures.
doi:10.1128/AEM.05925-11
PMCID: PMC3209001  PMID: 21948825
11.  H-NS Silences gfp, the Green Fluorescent Protein Gene: gfpTCD Is a Genetically Remastered gfp Gene with Reduced Susceptibility to H-NS-Mediated Transcription Silencing and with Enhanced Translation ▿ §  
Journal of Bacteriology  2010;192(18):4790-4793.
The bacterial nucleoid-associated protein H-NS, which preferentially targets and silences A+T-rich genes, binds the ubiquitous reporter gene gfp and dramatically reduces local transcription. We have redesigned gfp to reduce H-NS-mediated transcription silencing and simultaneously improve translation in vivo without altering the amino acid sequence of the GFP protein.
doi:10.1128/JB.00531-10
PMCID: PMC2937413  PMID: 20639321
12.  Effect of Cassava Hay and Rice Bran Oil Supplementation on Rumen Fermentation, Milk Yield and Milk Composition in Lactating Dairy Cows 
Four crossbred (75% Holstein Friesian) lactating dairy cows, with an average live weight of 418±5 kg and 36±10 d in milk were randomly assigned according to a 2×2 factorial arrangement in a 4×4 Latin square design to evaluate the effects of cassava hay (CH) and rice bran oil (RBO) on feed intake, nutrient digestibility, ruminal fermentation, milk yield, and milk composition. Factor A was non-supplementation or supplementation with CH in the concentrate. Factor B was supplementation with RBO at 0% or 4% in the concentrate mixture. The four dietary treatments were (T1) control (Concentrate with non-CH plus 0% RBO; C), (T2) Concentrate with CH plus 0% RBO (CH), (T3) Concentrate with non-CH plus 4% RBO (RBO), and (T4) Concentrate with CH plus 4% RBO (CHRBO). The cows were offered concentrate, at a ratio of concentrate to milk production of 1:2, and urea-lime treated rice straw was fed ad libitum. Urea-lime treated rice straw involved 2.5 g urea and 2.5 g Ca(OH)2 (purchased as hydrated lime) in 100 ml water, the relevant volume of solution was sprayed onto a 100 g air-dry (91% DM) straw, and then covering the stack with a plastic sheet for a minimum of 10 d before feeding directly to animals. The CH based concentrate resulted in significantly higher roughage intake and total DM intake expressed as a percentage of BW (p<0.05). Ruminal pH, NH3-N, BUN and total VFA did not differ among treatments, while RBO supplementation increased propionate, but decreased acetate concentration (p<0.05). Furthermore, the population of total ruminal bacteria was significantly lower on the RBO diet (p<0.05). In contrast, the total ruminal bacteria and cellulolytic bacteria on the CH diet were higher than on the other treatments. Supplementation with CH increased (p<0.05) F. succinogens and R. flavefaciens populations, whereas the populations of B. fibrisolvens and M. elsdenii were increased on the RBO diet. In addition, supplementation with CH and RBO had no effect on milk production and composition in dairy cows, while fatty acid composition of milk was influenced by RBO supplementation, and resulted in significantly lower (p<0.05) concentrations of both short-chain and medium-chain FA, and increased (p<0.05) the proportion of long-chain FA in milk fat, as well as significantly increased cis-9, trans-11 CLA and total CLA. In conclusion, RBO or CH exhibited specific effects on DM, rumen fermentation, microbial population, milk yield and composition in lactating dairy cows, which were not interactions between CH and RBO in the diets. Feeding lactating dairy cows with RBO could improve fatty acid in milk fat by increasing cis-9, trans-11 CLA.
doi:10.5713/ajas.2012.12051
PMCID: PMC4093022  PMID: 25049491
Cassava Hay; Rice Bran Oil; Rumen Fermentation; Milk Yield and Composition; Lactating Dairy Cows
13.  Bovine viral diarrhea virus in free-ranging wild ruminants in Switzerland: low prevalence of infection despite regular interactions with domestic livestock 
Background
In the frame of an eradication program for bovine viral diarrhea (BVD) in Swiss livestock, the question was raised whether free-ranging wildlife could threaten the success of this sanitary measure. Therefore, we conducted serological and virological investigations on BVD virus (BVDV) infections in the four indigenous wild ruminant species (roe deer, red deer, Alpine chamois and Alpine ibex) from 2009 to 2011, and gathered information on interactions between wild and domestic ruminants in an alpine environment by questionnaire survey.
Results
Thirty-two sera out of 1’877 (1.7%, 95% confidence interval [CI] 1.2-2.4) were seropositive for BVDV, and a BVDV1 sub genotype h virus was found in a seropositive chamois (0.05%, 95% CI 0.001-0.3). The seropositive animals originated from sub-alpine or alpine regions and significantly more seropositive red deer, chamois and ibex than roe deer were found. There were no statistically significant differences between sampling units, age classes, genders, and sampling years. The obtained prevalences were significantly lower than those documented in livestock, and most positive wild ruminants were found in proximity of domestic outbreaks. Additionally, BVDV seroprevalence in ibex was significantly lower than previously reported from Switzerland. The survey on interspecific interactions revealed that interactions expected to allow BVDV transmission, from physical contacts to non-simultaneous use of the same areas, regularly occur on pastures among all investigated ruminant species. Interactions involving cervids were more often observed with cattle than with small ruminants, chamois were observed with all three domestic species, and ibex interacted mostly with small ruminants. Interactions related to the use of anthropogenic food sources were frequently observed, especially between red deer and cattle in wintertime.
Conclusions
To our knowledge, this is the first report of BVDV RNA isolated from an Alpine chamois. Nevertheless, our results suggest that BVDV infections are only sporadic in Swiss wild ruminants, despite regular occurrence of interactions with potentially infected livestock. Overall, serological, virological and ethological data indicate that wildlife is currently an incidental spill-over host and not a reservoir for BVDV in Switzerland.
doi:10.1186/1746-6148-8-204
PMCID: PMC3514304  PMID: 23107231
Bovine viral diarrhea virus; Epidemiology; Interactions; Livestock; Seroprevalence; Switzerland; Wild ruminants
14.  Effects of different sources of carbohydrates on intake, digestibility, chewing, and performance of Holstein dairy cows 
To investigate the effects of different sources of carbohydrates on intake, digestibility, chewing, and performance, nine lactating Holstein dairy cows (day in milk= 100±21 d; body weight=645.7 ± 26.5 kg) were allotted to a 3 × 3 Latin square design at three 23-d periods. The three treatments included 34.91% (B), 18.87% (BC), and 18.86% (BB) barley that in treatment B was partially replaced with only corn or corn plus beet pulp in treatments BC and BB, respectively. The concentration of starch and neutral detergent soluble carbohydrate varied (22.2, 20.2, and 14.5; 13.6, 15.9, and 20.1% of DM in treatments B, BC, and BB, respectively). Cows in treatment BB showed a higher DMI and improved digestibility of DM, NDF, and EE compared with treatments B or BC. Ruminal pH was higher in cows fed on BB (6.83) compared with those that received B or BC treatments (6.62 and 6.73, respectively). A lower proportion of propionate accompanied the higher pH in the BB group; however, a greater proportion of acetate and acetate: propionate ratio was observed compared with cows fed either on the B or BC diet. Moreover, cows fed on the BB diet showed the lowest ruminal passage rate and longest ruminal and total retention time. Eating time did not differ among treatments, rumination time was greater among cows fed on the BB diet compared with the others, whereas total chewing activity was greater than those fed on BC, but similar to those fed on B. The treatments showed no effect on milk yield. Partially replacing barley with corn or beet pulp resulted in an increase in milk fat and a lower protein concentration. Changing dietary NFC with that of a different degradability thus altered intake, chewing activity, ruminal environment, retention time or passage rate, and lactation performance. The results of this study showed that beet pulp with a higher NDF and a detergent-soluble carbohydrate or pectin established a more consistent ruminal mat than barley and corn, thus resulting in higher mean retention time and chewing activity, whereas no changes in 3.5% FCM and milk fat were observed.
doi:10.1186/2049-1891-5-6
PMCID: PMC3912492  PMID: 24410961
Chewing activity; Dairy cow; Detergent-soluble carbohydrate; Fiber; Neutral detergent fiber; Physically effective fiber; Ruminal characteristics
15.  Evaluation of Coarsely Ground Wheat as a Replacement for Ground Corn in the Diets of Lactating Dairy Cows 
Eight multiparous Holstein cows (569±47 kg of BW; 84±17 DIM) were used to evaluate the effects of different levels of coarsely ground wheat (CGW) as replacements for ground corn (GC) in diets on feed intake and digestion, ruminal fermentation, lactation performance, and plasma metabolites profiles in dairy cows. The cows were settled in a replicated 4×4 Latin square design with 3-wk treatment periods; four cows in one of the replicates were fitted with rumen cannulas. The four diets contained 0, 9.6, 19.2, and 28.8% CGW and 27.9, 19.2, 9.6, and 0% GC on dry matter (DM) basis, respectively. Increasing dietary levels of CGW, daily DM intake tended to increase quadratically (p = 0.07); however, apparent digestibility of neutral detergent fiber (NDF) and acid detergent fiber (ADF) were significantly decreased (p<0.01) in cows fed the 28.8% CGW diets. Ruminal pH remained in the normal physiological range for all dietary treatments at all times, except for the 28.8% CGW diets at 6 h after feeding; moreover, increasing dietary levels of CGW, the daily mean ruminal pH decreased linearly (p = 0.01). Increasing the dietary levels of CGW resulted in a linear increase in ruminal propionate (p<0.01) and ammonia nitrogen (NH3-N) (p = 0.06) concentration, while ruminal acetate: propionate decreased linearly (p = 0.03) in cows fed the 28.8% CGW diets. Milk production was not affected by diets; however, percentage and yield of milk fat decreased linearly (p = 0.02) when the level of CGW was increased. With increasing levels of dietary CGW, concentrations of plasma beta-hydroxybutyric acid (BHBA) (p = 0.07) and cholesterol (p<0.01) decreased linearly, whereas plasma glucose (p = 0.08), insulin (p = 0.02) and urea nitrogen (p = 0.02) increased linearly at 6 h after the morning feeding. Our results indicate that CGW is a suitable substitute for GC in the diets of dairy cows and that it may be included up to a level of 19.2% of DM without adverse effects on feed intake and digestion, ruminal fermentation, lactation performance, and plasma metabolites if the cows are fed fiber-sufficient diets.
doi:10.5713/ajas.2013.13059
PMCID: PMC4093492  PMID: 25049874
Dairy Cows; Digestion; Lactation; Plasma Metabolites; Rumen Fermentation; Wheat
16.  Bacterial communities in the rumen of Holstein heifers differ when fed orchardgrass as pasture vs. hay 
The rich and diverse microbiota of the rumen provides ruminant animals the capacity to utilize highly fibrous feedstuffs as their energy source, but there is surprisingly little information on the composition of the microbiome of ruminants fed all-forage diets, despite the importance of such agricultural production systems worldwide. In three 28-day periods, three ruminally-cannulated Holstein heifers sequentially grazed orchardgrass pasture (OP), then were fed orchardgrass hay (OH), then returned to OP. These heifers displayed greater shifts in ruminal bacterial community composition (determined by automated ribosomal intergenic spacer analysis and by pyrotag sequencing of 16S rRNA genes) than did two other heifers maintained 84 d on the same OP. Phyla Firmicutes and Bacteroidetes dominated all ruminal samples, and quantitative PCR indicated that members of the genus Prevotella averaged 23% of the 16S rRNA gene copies, well below levels previously reported with cows fed total mixed rations. Differences in bacterial community composition and ruminal volatile fatty acid (VFA) profiles were observed between the OP and OH despite similarities in gross chemical composition. Compared to OP, feeding OH increased the molar proportion of ruminal acetate (P = 0.02) and decreased the proportion of ruminal butyrate (P < 0.01), branched-chain VFA (P < 0.01) and the relative population size of the abundant genus Butyrivibrio (P < 0.001), as determined by pyrotag sequencing. Despite the low numbers of animals examined, the observed changes in VFA profile in the rumens of heifers on OP vs. OH are consistent with the shifts in Butyrivibrio abundance and its known physiology as a butyrate producer that ferments both carbohydrates and proteins.
doi:10.3389/fmicb.2014.00689
PMCID: PMC4260508  PMID: 25538699
rumen microbiology; bacterial community composition; pasture; hay; forage; volatile fatty acids
17.  Diverse captive non-human primates with phytanic acid-deficient diets rich in plant products have substantial phytanic acid levels in their red blood cells 
Background
Humans and rodents with impaired phytanic acid (PA) metabolism can accumulate toxic stores of PA that have deleterious effects on multiple organ systems. Ruminants and certain fish obtain PA from the microbial degradation of dietary chlorophyll and/or through chlorophyll-derived precursors. In contrast, humans cannot derive PA from chlorophyll and instead normally obtain it only from meat, dairy, and fish products.
Results
Captive apes and Old world monkeys had significantly higher red blood cell (RBC) PA levels relative to humans when all subjects were fed PA-deficient diets. Given the adverse health effects resulting from PA over accumulation, we investigated the molecular evolution of thirteen PA metabolism genes in apes, Old world monkeys, and New world monkeys. All non-human primate (NHP) orthologs are predicted to encode full-length proteins with the marmoset Phyh gene containing a rare, but functional, GA splice donor dinucleotide. Acox2, Scp2, and Pecr sequences had amino acid positions with accelerated substitution rates while Amacr had significant variation in evolutionary rates in apes relative to other primates.
Conclusions
Unlike humans, diverse captive NHPs with PA-deficient diets rich in plant products have substantial RBC PA levels. The favored hypothesis is that NHPs can derive significant amounts of PA from the degradation of ingested chlorophyll through gut fermentation. If correct, this raises the possibility that RBC PA levels could serve as a biomarker for evaluating the digestive health of captive NHPs. Furthermore, the evolutionary rates of the several genes relevant to PA metabolism provide candidate genetic adaptations to NHP diets.
doi:10.1186/1476-511X-12-10
PMCID: PMC3571895  PMID: 23379307
Phytanic acid; Chlorophyll; Old world monkeys; New world monkeys; Peroxisome
18.  Effects of Combining Feed Grade Urea and a Slow-release Urea Product on Characteristics of Digestion, Microbial Protein Synthesis and Digestible Energy in Steers Fed Diets with Different Starch:ADF Ratios 
As a result of the cost of grains, the replacement of grains by co-products (i.e. DDGS) in feedlot diets is a common practice. This change produces diets that contain a lower amount of starch and greater amount of fibre. Hypothetically, combining feed grade urea (U) with slow release urea (Optigen) in this type of diet should elicit a better synchrony between starch (high-rate of digestion) and fibre (low-rate of digestion) promoting a better microbial protein synthesis and ruminal digestion with increasing the digestible energy of the diet. Four cannulated Holstein steers (213±4 kg) were used in a 4×4 Latin square design to examine the combination of Optigen and U in a finishing diet containing different starch:acid detergent fibre ratios (S:F) on the characteristics of digestive function. Three S:F ratios (3.0, 4.5, and 6.0) were tested using a combination of U (0.80%) and Optigen (1.0%). Additionally, a treatment of 4.5 S:F ratio with urea (0.80% in ration) as the sole source of non-protein nitrogen was used to compare the effect of urea combination at same S:F ratio. The S:F ratio of the diet was manipulated by replacing the corn grain by dried distillers grain with solubles and roughage. Urea combination did not affect ruminal pH. The S:F ratio did not affect ruminal pH at 0 and 2 h post-feeding but, at 4 and 6 h, the ruminal pH decreased as the S:F ratio increased (linear, p<0.05). Ruminal digestion of OM, starch and feed N were not affected by urea combination or S:F ratio. The urea combination did not affect ADF ruminal digestion. ADF ruminal digestion decreased linearly (p = 0.02) as the S:F ratio increased. Compared to the urea treatment (p<0.05) and within the urea combination treatment (quadratic, p<0.01), the flow of microbial nitrogen (MN) to the small intestine and ruminal microbial efficiency were greater for the urea combination at a S:F ratio of 4.5. Irrespective of the S:F ratio, the urea combination improved (2.8%, p = 0.02) postruminal N digestion. As S:F ratio increased, OM digestion increased, but ADF total tract digestion decreased. The combination of urea at 4.5 S:F improved (2%, p = 0.04) the digestible energy (DE) more than expected. Combining urea and Optigen resulted in positive effects on the MN flow and DE of the diet, but apparently these advantages are observed only when there is a certain proportion of starch:ADF in the diet.
doi:10.5713/ajas.2013.13395
PMCID: PMC4093204  PMID: 25049942
Slow-release Urea; Finishing Diets; Steers; Digestion; Microbial Nitrogen
19.  The Influence of Feed Energy Density and a Formulated Additive on Rumen and Rectal Temperature in Hanwoo Steers 
The present study investigated the optimum blending condition of protected fat, choline and yeast culture for lowering of rumen temperature. The Box Benken experimental design, a fractional factorial arrangement, and response surface methodology were employed. The optimum blending condition was determined using the rumen simulated in vitro fermentation. An additive formulated on the optimum condition contained 50% of protected fat, 25% of yeast culture, 5% of choline, 7% of organic zinc, 6.5% of cinnamon, and 6.5% of stevioside. The feed additive was supplemented at a rate of 0.1% of diet (orchard grass:concentrate, 3:7) and compared with a control which had no additive. The treatment resulted in lower volatile fatty acid (VFA) concentration and biogas than the control. To investigate the effect of the optimized additive and feed energy levels on rumen and rectal temperatures, four rumen cannulated Hanwoo (Korean native beef breed) steers were in a 4×4 Latin square design. Energy levels were varied to low and high by altering the ratio of forage to concentrate in diet: low energy (6:4) and high energy (4:6). The additive was added at a rate of 0.1% of the diet. The following parameters were measured; feed intake, rumen and rectal temperatures, ruminal pH and VFA concentration. This study was conducted in an environmentally controlled house with temperature set at 30°C and relative humidity levels of 70%. Steers were housed individually in raised crates to facilitate collection of urine and feces. The adaptation period was for 14 days, 2 days for sampling and 7 days for resting the animals. The additive significantly reduced both rumen (p<0.01) and rectal temperatures (p<0.001) without depressed feed intake. There were interactions (p<0.01) between energy level and additive on ruminal temperature. Neither additive nor energy level had an effect on total VFA concentration. The additive however, significantly increased (p<0.01) propionate and subsequently had lower acetate:propionate (A/P) ratios than non-additive supplementation. High concentrate diets had significantly lower pH. Interactions between energy and additive were observed (p<0.01) in ammonia nitrogen production. Supplementation of diets with the additive resulted in lower rumen and rectal temperatures, hence the additive showed promise in alleviating undesirable effects of heat stress in cattle.
doi:10.5713/ajas.2014.14562
PMCID: PMC4213712  PMID: 25358327
Beef Cattle; Feed Additive; Heat Stress; Rectal Temperature; Rumen Temperature
20.  The allometry of patch selection in ruminants. 
An axiomatic feature of food consumption by animals is that intake rate and prey abundance are positively related. While this has been demonstrated rigorously for large herbivores, it is apparent from patch selection trials that grazers paradoxically tend to prefer short, sparse swards to tall, dense swards. Indeed, migratory herbivores often shift from areas of high to low sward biomass during the growing season. As nutritional quality is an inverse function of grass abundance, herbivores appear to sacrifice short-term intake for nutritional gains obtainable by eating sparse forage of higher quality. Explicit models of this trade-off suggest that individual ruminants maximize daily rates of energy gain by choosing immature swards of intermediate biomass. As body mass is related positively to both ruminant cropping rates and digestibility, there should be an allometric link between grass abundance and energy maximization, providing a tool for predicting patterns of herbivore habitat selection. We used previously published studies to develop a synthetic model of trade-offs between forage abundance and quality predicting that optimal sward biomass should scale allometrically with body size. The model predicts size-related variation in habitat selection observed in a guild of grazing ungulates in the Serengeti ecosystem.
PMCID: PMC1690547  PMID: 10722215
21.  Resistance of rumen bacteria murein to bovine gastric lysozyme 
BMC Ecology  2004;4:7.
Background
Lysozymes, enzymes mostly associated with defence against bacterial infections, are mureinolytic. Ruminants have evolved a gastric c type lysozyme as a digestive enzyme, and profit from digestion of foregut bacteria, after most dietary components, including protein, have been fermented in the rumen. In this work we characterized the biological activities of bovine gastric secretions against membranes, purified murein and bacteria.
Results
Bovine gastric extract (BGE) was active against both G+ and G- bacteria, but the effect against Gram- bacteria was not due to the lysozyme, since purified BGL had only activity against Gram+ bacteria. We were unable to find small pore forming peptides in the BGE, and found that the inhibition of Gram negative bacteria by BGE was due to an artefact caused by acetate. We report for first time the activity of bovine gastric lysozyme (BG lysozyme) against pure bacterial cultures, and the specific resistance of some rumen Gram positive strains to BGL.
Conclusions
Some Gram+ rumen bacteria showed resistance to abomasum lysozyme. We discuss the implications of this finding in the light of possible practical applications of such a stable antimicrobial peptide.
doi:10.1186/1472-6785-4-7
PMCID: PMC420471  PMID: 15137912
22.  Comparisons of ruminal fermentation characteristics and microbial populations in bison and cattle. 
Applied and Environmental Microbiology  1988;54(10):2510-2514.
Ruminal microbial populations, fermentation characteristics, digestibility, and liquid flow rates in two ruminally cannulated bison and two ruminally cannulated Hereford steers fed a prairie hay diet were compared. No significant differences in anaerobic bacterial counts, volatile fatty acid concentrations, or ruminal pHs were evident between bison and cattle. Also, no significant differences in neutral detergent fiber digestibility, indigestible fiber retention time, or intake were detected between bison and cattle, although cattle had higher levels (P less than 0.08) of ruminal dry matter and indigestible fiber than bison. Bison had a smaller (P = .02) ruminoreticular volume, faster liquid dilution rates, and faster liquid turnover times than cattle. The average ruminal ammonia nitrogen concentration was higher (P = 0.02) in bison (1.17 mg/dl) than in cattle (0.79 mg/dl). Total ciliate protozoal counts and cell volume were greater (P = 0.07) in bison (32.8 x 10(4)/g and 407.1 x 10(-4) ml/g, respectively) than in cattle (15.7 x 10(4)/g and 162.2 x 10(-4) ml/g, respectively). Bison harbored higher (P less than 0.02) numbers of Dasytricha spp., Eudiplodinium maggii, Eudiplodinium bursa, and Epidinium spp. than cattle and possessed a type B protozoan population. The cattle possessed a mixed type A-type B population that was characterized by Ophryoscolex spp. and Polyplastron spp. in association with low concentrations of Epidinium spp. and Eudiplodinium maggii.
PMCID: PMC204300  PMID: 3272131
23.  Prebiotic inulin: Useful dietary adjuncts to manipulate the livestock gut microflora 
In recent years, there has been a growing appreciation on the relevance of gastrointestinal microflora in both ruminants and non-ruminants owing to revelation of their role in several physiological functions including digestion, nutrient utilization, pathogen exclusion, gastrointestinal development, immunity system, gut gene expression and quality of animal products. The ban imposed on the use of antibiotics and hormones in feed has compelled animal researchers in finding an alternative which could overcome the issues of conventional feed additives. Though the concept of prebiotic was evolved keeping in mind the gastrointestinal flora of human beings, presently animal researchers are exploring the efficiency of prebiotic (inulin) for modulating the gut ecosystem of both ruminants and non-ruminants. It was revealed that prebiotic inulin is found to exhibit desirable changes in the gut of non-ruminants like poultry, swine, rabbit etc for augmenting gut health and improvement of product quality. Similarly, in ruminants the prebiotic reduces rumen ammonia nitrogen, methane production, increase microbial protein synthesis and live weight gains in calves. Unlike other feed additives, prebiotic exhibits its effect in multipronged ways for overall increase in the performances of the animals. In coming days, it is expected that prebiotics could be the part of diets in both ruminants and non-ruminants for enabling modulation of gut microflora vis a vis animals productivity in ecological ways.
doi:10.1590/S1517-83822013005000023
PMCID: PMC3804171  PMID: 24159277
prebiotic; inulin; mechanism of action; livestock
24.  Analysis of sporadic neuroendocrine tumours of the enteropancreatic system by comparative genomic hybridisation 
Gut  2001;48(4):536-541.
BACKGROUND—Chromosomal instability is observed in a wide spectrum of human cancer syndromes. However, to date, little is known of the characteristic genetic changes in sporadic neuroendocrine tumours of the gastroenteropancreatic system.
AIMS AND METHOD—We have studied copy number aberrations (CNAs) in 26 sporadic neuroendocrine tumours of the enteropancreatic system (12 foregut and 14 midgut tumours) by comparative genomic hybridisation (CGH), allowing simultaneous evaluation of the entire tumour genome.
RESULTS—Nearly all tumours (25/26; that is, 96%) showed chromosomal imbalances, including full chromosomal aneuploidies, losses and gains of chromosome arms, interstitial deletions, and amplifications. Whereas gains of chromosomes 4, 5, and 19 were found in both foregut and midgut tumours, gains of chromosomes 20q (58%), 19 (50%), as well as 17p (50%), and partial losses of chromosomes 1p (42%), 2q (42%), 3p, 4q, and 6q (25% each) were frequently observed only in foregut tumours. In contrast, midgut tumours displayed less CNAs. Gains were detected for chromosomes 17q and 19p (57%). Most frequent losses affected chromosomes 18 (43%) and 9p (21%).
CONCLUSIONS—The results of our CGH analyses revealed new distinct candidate regions in the human genome associated with sporadic neuroendocrine tumours. Some of the genetic alterations were shared by foregut and midgut tumours while others discriminated between the two groups. Thus our results allude to the involvement of identical as well as discriminative genetic loci in tumorigenesis and progression of neuroendocrine neoplasms of the foregut and midgut. Based on these findings potential new candidate genes will be discussed.


Keywords: gastroenteropancreatic tumours; comparative genomic hybridisation; foregut; midgut
doi:10.1136/gut.48.4.536
PMCID: PMC1728244  PMID: 11247899
25.  Effect of cellulose fine structure on kinetics of its digestion by mixed ruminal microorganisms in vitro. 
The digestion kinetics of a variety of pure celluloses were examined by using an in vitro assay employing mixed ruminal microflora and a modified detergent extraction procedure to recover residual cellulose. Digestion of all of the celluloses was described by a discontinuous first-order rate equation to yield digestion rate constants and discrete lag times. These kinetic parameters were compared with the relative crystallinity indices and estimated accessible surface areas of the celluloses. For type I celluloses having similar crystallinities and simple nonaggregating particle morphologies, the fermentation rate constants displayed a strong positive correlation (r2 = 0.978) with gross specific surface area; lag time exhibited a weaker, negative correlation (r2 = 0.930) with gross specific surface area. Crystallinity was shown to have a relatively minor effect on the digestion rate and lag time. Swelling of microcrystalline cellulose with 72 to 77% phosphoric acid yielded substrates which were fermented slightly more rapidly than the original material. However, treatment with higher concentrations of phosphoric acid resulted in a more slowly fermented substrate, despite a decrease in crystallinity and an increase in pore volume. This reduced fermentation rate was apparently due to the partial conversion of the cellulose from the type I to the type II allomorph, since mercerized (type II) cellulose was also fermented more slowly, and only after a much longer lag period. The results are consistent with earlier evidence for the cell-associated nature of cellulolytic enzymes of ruminal bacteria and suggest that ruminal microflora do not rapidly adapt to utilization of celluloses with altered unit cell structures.
PMCID: PMC184744  PMID: 2403252

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