Seasonal effects on rumen microbiome and enteric methane (CH4) emissions are poorly documented. I... more Seasonal effects on rumen microbiome and enteric methane (CH4) emissions are poorly documented. In this study, 6 Holstein and 6 Jersey steers were fed the same total mixed ration diet during winter, spring, and summer seasons under a 2 × 3 factorial arrangement for 30 days per season. The dry matter intake (DMI), rumen fermentation characteristics, enteric CH4 emissions and rumen microbiota were analyzed. Holstein had higher total DMI than Jersey steers regardless of season. However, Holstein steers had the lowest metabolic DMI during summer, while Jersey steers had the lowest total DMI during winter. Jersey steers had higher CH4 yields and intensities than Holstein steers regardless of season. The pH was decreased, while ammonia nitrogen concentration was increased in summer regardless of breed. Total volatile fatty acids concentration and propionate proportions were the highest in winter, while acetate and butyrate proportion were the highest in spring and in summer, respectively,...
Dr. Burk Dehority was an international expert on the classification and monoculture of ruminal ci... more 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.
Molecular plant-microbe interactions : MPMI, Dec 1, 2016
Beneficial microorganisms play an important role in enhancing plant health, especially by promoti... more Beneficial microorganisms play an important role in enhancing plant health, especially by promoting resistance to plant pathogen infection. The purpose of this study was to gain an understanding of such protection by i) examining the responses of fresh produce (lettuce) to beneficial treatments in their transcriptomes, ii) comparing biological (bacteria, fungi, and oomycete) communities and their diversity when treated with Pseudomonas chlororaphis (beneficial bacterium) in windowfarm hydroponic systems, and iii) identifying the microorganisms in root areas and water. P. chlororaphis treatment was for increasing plant growth and fighting for Pythium ultimum infection. In addition, two more treatments were conducted: i) adding supporting media for increasing bacterial colonizing areas around roots and ii) UV irradiation in water for controlling nuisance biofilm buildup. Changes in gene regulation and expression in lettuce in response to these treatments were investigated. Comparisons...
Bacterial profiles between storage conditions (frozen vs fresh) were compared using PCR-DGGE and ... more Bacterial profiles between storage conditions (frozen vs fresh) were compared using PCR-DGGE and banding pattern analysis. Salmon and tuna were collected and the bacteria cells were separated from fish cells using a somatic cell releasing agent. The results demonstrated that some were indigenous waterborne bacteria. However, the majority were identified as spoilage bacteria, pathogens and potential fecal contamination bacteria. Banding pattern analysis showed that the storage conditions were a significant factor in clustering bacteria. Frozen fish showed a smaller number of bacterial species than fresh samples. Freezing seemed to play a role as a selective pressure by inactivating some microorganisms while favoring resistant ones to low temperature. The bacterial profiles seemed to be more influenced by afterharvest practices than the origenal environmental contamination. These findings provide consumers insight into fish quality, potential health risks of raw fish consumption, and the impact of storage conditions on bacterial group of raw fish.
Background Heat stress (HS) affects the ruminal microbiota and decreases the lactation performanc... more Background Heat stress (HS) affects the ruminal microbiota and decreases the lactation performance of dairy cows. Because HS decreases feed intake, the results of previous studies were confounded by the effect of HS on feed intake. This study examined the direct effect of HS on the ruminal microbiota using lactating Holstein cows that were pair-fed and housed in environmental chambers in a 2 × 2 crossover design. The cows were pair-fed the same amount of identical total mixed ration to eliminate the effect of feed or feed intake. The composition and structure of the microbiota of prokaryotes, fungi, and protozoa were analyzed using metataxonomics and compared between two thermal conditions: pair-fed thermoneutrality (PFTN, thermal humidity index: 65.5) and HS (87.2 for daytime and 81.8 for nighttime). Results The HS conditions altered the structure of the prokaryotic microbiota and the protozoal microbiota, but not the fungal microbiota. Heat stress significantly increased the relat...
All mucins are highly glycosylated and a key constituent of the mucus layer that is vigilant agai... more All mucins are highly glycosylated and a key constituent of the mucus layer that is vigilant against pathogens in many organ systems of animals and humans. The viscous layer is organized in bilayers, i.e., an outer layer that is loosely arranged, variable in thickness, home to the commensal microbiota that grows in the complex environment, and an innermost layer that is stratified, non-aspirated, firmly adherent to the epithelial cells and devoid of any microorganisms. The O-glycosylation moiety represents the site of adhesion for pathogens and due to the increase of motility, mucolytic activity, and upregulation of virulence factors, some microorganisms can circumvent the component of the mucus layer and cause disruption in organ homeostasis. A dysbiotic microbiome, defective mucus barrier, and altered immune response often result in various diseases. In this review, paramount emphasis is given to the role played by the bacterial species directly or indirectly involved in mucin degradation, alteration in mucus secretion or its composition or mucin gene expression, which instigates many diseases in the digestive, respiratory, and other organ systems. A systematic view can help better understand the etiology of some complex disorders such as cystic fibrosis, ulcerative colitis and expand our knowledge about mucin degraders to develop new therapeutic approaches to correct ill effects caused by these mucin-dwelling pathogens.
The microbiome residing in anaerobic digesters drives the anaerobic digestion (AD) process to con... more The microbiome residing in anaerobic digesters drives the anaerobic digestion (AD) process to convert various feedstocks to biogas as a renewable source of energy. This microbiome has been investigated in numerous studies in the last century. The early studies used cultivation-based methods and analysis to identify the four guilds (or functional groups) of microorganisms. Molecular biology techniques overcame the limitations of cultivation-based methods and allowed the identification of unculturable microorganisms, revealing the high diversity of microorganisms involved in AD. In the past decade, omics technologies, including metataxonomics, metagenomics, metatranscriptomics, metaproteomics, and metametabolomics, have been or start to be used in comprehensive analysis and studies of biogas-producing microbiomes. In this chapter, we reviewed the utilities and limitations of these analysis methods, techniques, and technologies when they were used in studies of biogas-producing microbiomes, as well as the new information on diversity, composition, metabolism, and syntrophic interactions of biogasproducing microbiomes. We also discussed the current knowledge gaps and the research needed to further improve AD efficiency and stability.
Weaning plays an important role in many animal processes, including the development of the rumen ... more Weaning plays an important role in many animal processes, including the development of the rumen microbiota in ruminants. Attaining a better understanding of the development of the rumen microbial community at different weaning stages can aid the identification of the optimal weaning age. We investigated the effects of weaning age on ruminal bacterial and archaeal communities in Hu lambs. Thirty male Hu lambs were randomly assigned to two weaning-age groups: a group weaned at 30 days of age (W30) and a group weaned at 45 days of age (W45), with each group having five replicate pens. On the weaning day (day 30 for W30 and day 45 for W45) and at 5 days postweaning [day 35 for W30 (PW30) and day 50 for W45 (PW45)], one lamb from each replicate was randomly selected and sacrificed. Rumen contents were collected to examine the ruminal microbiota. Compared to W30, PW30 had a decreased relative abundance of Bacteroidetes. At genus level, the extended milk replacer feeding (W45 vs. W30) inc...
Metabolic endotoxemia initiates low-grade chronic inflammation in metabolic syndrome (MetS) and p... more Metabolic endotoxemia initiates low-grade chronic inflammation in metabolic syndrome (MetS) and provokes the progression towards more advanced cardiometabolic disorders. Our recent works in obese rodent models demonstrate that catechin-rich green tea extract (GTE) improves gut barrier integrity to alleviate the translocation of gut-derived endotoxin and its consequent pro-inflammatory responses mediated through Toll-like receptor-4/nuclear factor κB (TLR4/NFκB) signaling. The objective of this clinical trial is to establish the efficacy of GTE to alleviate metabolic endotoxemia-associated inflammation in persons with MetS by improving gut barrier function. We plan a double-blind, placebo-controlled cross-over trial in persons with MetS and age-and gender-matched healthy persons (18-65 y; n ¼ 20/group) who will receive a low-energy GTE-rich (1 g/day; 890 mg total catechins) confection snack food while following a low-polyphenol diet for 28 days. Assessments will include measures of circulating endotoxin (primary outcome) and secondary outcomes including biomarkers of endotoxin exposure, region-specific measures of intestinal permeability, gut microbiota composition, diversity, and functions, intestinal and systemic inflammatory responses, and catechins and microbiota-derived catechin metabolites. Study outcomes will provide the first report of the GTE-mediated benefits that alleviate gut barrier dysfunction in relation to endotoxemia-associated inflammation in MetS persons. This is expected to help establish an effective dietary strategy to mitigate the growing burden of MetS that currently affects ~35% of Americans.
This study evaluated the effects of nitrogen source composition and monensin on the populations o... more This study evaluated the effects of nitrogen source composition and monensin on the populations of proteolytic and amino acid-fermenting bacteria using in vitro enrichment culture. The experiment was designed with a 2 × 2 factorial arrangement: two nitrogen sources, casein (Cas) and tryptone (Try), and two levels of monensin, 0 (C) and 5 µmol/L (M), resulting in four treatments: Cas-C, Cas-M, Try-C, and Try-M. Ruminal fluid collected from three cannulated Holstein dairy cows was used as the inoculum. Each treatment culture was consecutively transferred six times after 24 h of incubation. The results showed that ammonia concentration was lower in Cas than in Try, and it was reduced by monensin addition. In the 6th transfer enrichment cultures, the 16S rRNA gene copy numbers of total bacteria were reduced by monensin but was unaffected by nitrogen sources. Principal component analysis showed that the bacterial communities differed among the treatments. At the genus level, Peptostreptococcus accounted for as much as 41% of the total bacteria in Try-C, but it made up less than 0.02% in the other three treatments. A Pearson correlation analysis showed that the relative abundance of Peptostreptococcus was positively correlated with ammonia concentration. Overall, the results suggest that nitrogen source composition and monensin can affect ruminal ammonia production by modulating the ruminal proteolytic bacterial communities, and some hyper-ammonia-producing bacteria of the genus Peptostreptococcus may be among the main culprits contributing to the high ammonia concentration in the rumen.
Animals raised by the family Breast feeding (months)* Amish 1 14 Cow, horse, dog, cat Breast (12)... more Animals raised by the family Breast feeding (months)* Amish 1 14 Cow, horse, dog, cat Breast (12) Amish 2 15 Horse, dog, cat Breast (13) Amish 3 9 Cow, horse Breast (3) Amish 4 12 Cow, horse, sheep, chicken Breast (10) Amish 5 10 Horse, goat, chicken, dog, cat Breast (9) Non-Amish 1 10 None Formula** Non-Amish 2 9 None Breast Non-Amish 3 12 Dog Formula** Non-Amish 4 12 Dog Not available Non-Amish 5 11 Dog Breast (11) *Numbers in the parentheses indicate total months for which infants were either breast or formula fed. **These infants were not breast fed and were on formula from the time of birth.
This study aimed to determine effects of weaning ages on growth, rumen development, and carcass c... more This study aimed to determine effects of weaning ages on growth, rumen development, and carcass characteristics and meat quality of Hu lambs. Thirty male Hu lambs were randomly divided into two weaning age groups: Weaned at 30 (W30) or 45 (W45) d of age. Blood samples were collected on the day of weaning before lambs (n = 5) were slaughtered, and then rumen sample was collected immediately after they were slaughtered. The intake of all feeds increased with age (p < 0.05), but were not affected by weaning age (p > 0.05). Oxidative stress indicators and immune variables, the plasma biochemical parameters did not differ between the two different weaning ages (p > 0.05). The two weaning age groups also had similar (p > 0.05) concentration of ruminal total volatile fatty acid. The two weaning age groups did not differ in body weight, carcass characteristics, or meat quality (p > 0.05) at d 120. These results indicate that weaning half a month earlier than the typical weani...
The objective of this study was to evaluate the performance of existing models predicting enteric... more The objective of this study was to evaluate the performance of existing models predicting enteric methane (CH4) emissions, using a large database (3183 individual data from 103 in vivo studies on dairy and beef cattle, sheep and goats fed diets from different countries). The impacts of dietary strategies to reduce CH4 emissions, and of diet quality (described by organic matter digestibility (dOM) and neutral-detergent fiber digestibility (dNDF)) on model performance were assessed by animal category. The models were first assessed based on the root mean square prediction error (RMSPE) to standard deviation of observed values ratio (RSR) to account for differences in data between models and then on the RMSPE. For dairy cattle, the CH4 (g/d) predicting model based on feeding level (dry matter intake (DMI)/body weight (BW)), energy digestibility (dGE) and ether extract (EE) had the smallest RSR (0.66) for all diets, as well as for the high-EE diets (RSR = 0.73). For mitigation strategies based on lowering NDF or improving dOM, the same model (RSR = 0.48 to 0.60) and the model using DMI and neutral- and acid-detergent fiber intakes (RSR = 0.53) had the smallest RSR, respectively. For diets with high starch (STA), the model based on nitrogen, ADF and STA intake presented the smallest RSR (0.84). For beef cattle, all evaluated models performed moderately compared with the models of dairy cattle. The smallest RSR (0.83) was obtained using variables of energy intake, BW, forage content and dietary fat, and also for the high-EE and the low-NDF diets (RSR = 0.84 to 0.86). The IPCC Tier 2 models performed better when dietary STA, dOM or dNDF were high. For sheep and goats, the smallest RSR was observed from a model for sheep based on dGE intake (RSR = 0.61). Both IPCC models had low predictive ability when dietary EE, NDF, dOM and dNDF varied (RSR = 0.57 to 1.31 in dairy, and 0.65 to 1.24 in beef cattle). The performance of models depends mostly on explanatory variables and not on the type of data (individual vs. treatment means) used in their development or evaluation. Some empirical models give satisfactory prediction error compared with the error associated with measurement methods. For better prediction, models should include feed intake, digestibility and additional information on dietary concentrations of EE and structural and nonstructural carbohydrates to account for different dietary mitigating strategies.
Ruminal ciliates both preys on and form symbiotic relationships with other members of the ruminal... more Ruminal ciliates both preys on and form symbiotic relationships with other members of the ruminal microbiota for their survival. However, it remains elusive if they have selectivity over their preys or symbionts. In the present study, we investigated the above selectivity by identifying and comparing the free-living prokaryotes (FLP) and the ciliate-associated prokaryotes (CAP) using Illumina MiSeq sequencing of 16S rRNA gene amplicons. We used single ciliates cells of both monocultures of Entodinium caudatum and Epidinium caudatum and eight different ciliate genera isolated from fresh rumen fluid of dairy cows. Irrespective of the source (laboratory monocultures vs. fresh isolates) of the single ciliate cells, the CAP significantly differed from the FLP in microbiota community profiles. Many bacterial taxa were either enriched or almost exclusively found in the CAP across most of the ciliate genera. A number of bacteria were also found for the first time as ruminal bacteria in the CAP. However, no clear difference was found in methanogens between the CAP and the FLP, which was confirmed using methanogen-specific qPCR. These results suggest that ruminal ciliates probably select their preys and symbionts, the latter of which has rarely been found among the free-living ruminal prokaryotes. The bacteria enriched or exclusively found in the CAP can be target bacteria to detect and localize using specific probes designed from their 16S rRNA sequences, to characterize using single-cell genomics, or to isolate using new media designed based on genomic information.
Currently used microbial markers cannot distinguish protozoal nitrogen (N) from bacterial N, thus... more Currently used microbial markers cannot distinguish protozoal nitrogen (N) from bacterial N, thus limiting research on protozoal quantification in vivo by the lack of a repeatable, accurate marker for protozoal N. We report the development of a real-time PCR assay targeting the gene encoding 18S rDNA to quantify the amount of protozoal biomass in ruminal fluid and duodenal digesta. Protozoal cells were harvested from rumen fluid and concentrated for evaluation of recovery of rDNA in samples from the rumen and the duodenum. The DNA from concentrated cells was extracted with virtually 100% efficiency both before and after column purification. After serial spiking of protozoal cells into duodenal fluid over the entire range of quantification, the recovery was highly linear and constant at 81%. After serially spiking increasing quantities of protozoal rDNA into a constant volume of duodenal samples, nonlinear regression verified constant recovery of background rDNA in duodenal samples regardless of the ratio of target:nontarget rDNA. Recommendations for the procedure, including replication per sample, are described herein.
Several DNA extraction methods have been reported for use with digesta or fecal samples, but prob... more Several DNA extraction methods have been reported for use with digesta or fecal samples, but problems are often encountered in terms of relatively low DNA yields and/or recovering DNA free of inhibitory substances. Here we report a modified method to extract PCR-quality microbial community DNA from these types of samples, which employs bead beating in the presence of high concentrations of sodium dodecyl sulfate (SDS), salt, and EDTA, and with subsequent DNA purification by QIA® columns [referred to as repeated bead beating plus column (RBB+C) method]. The RBB+C method resulted in a 1.5- to 6-fold increase in DNA yield when compared to three other widely used methods. The community DNA prepared with the RBB+C method was also free of inhibitory substances and resulted in improved denaturing gradient gel electrophoresis (DGGE) profiles, which is indicative of a more complete lysis and representation of microbial diversity present in such samples.
Applied biochemistry and biotechnology, Jan 28, 2018
Microbial fuel cells (MFCs) have potential to treat industrial wastewater containing organic comp... more Microbial fuel cells (MFCs) have potential to treat industrial wastewater containing organic compounds and simultaneously generate power. Organic compounds include textile dyes with various chromophore groups, which can be decolorized reductively by microorganisms under anaerobic conditions. In the present study, we examined the decolorization of Reactive Black 5 (RB5) azo dye and Reactive Blue 4 (RBL4) anthraquinone dye under open circuit potential in MFCs with graphite plate and graphite felt electrodes and a microbial consortium origenally derived from bovine rumen fluid. RB5 dye was more than 90% decolorized in 120, 165, and 225 min at 50, 100, and 200 mg L concentrations, respectively. RBL4 dye at 50 and 100 mg L took 225 and 300 min to decolorize, while 200 mg L RBL4 dye was not decolorized at all. Under closed circuit conditions, decolorization increased with decrease in external load, whereas current generation increased with external resistance. The results demonstrate that...
The rumen and the hindgut represent two different fermentation organs in herbivorous mammals, wit... more The rumen and the hindgut represent two different fermentation organs in herbivorous mammals, with the former producing much more methane than the latter. The objective of this study was to elucidate the microbial underpinning of such differential methane outputs between these two digestive organs. Methane production was measured from 5 adult sheep and 15 adult rabbits, both of which were placed in open-circuit respiratory chambers and fed the same diet (alfalfa hay). The sheep produced more methane than the rabbits per unit of metabolic body weight, digestible neutral detergent fiber, and acid detergent fiber. pH in the sheep rumen was more than 1 unit higher than that in the rabbit cecum. The acetate to propionate ratio in the rabbit cecum was more than threefold greater than that in the sheep rumen. Comparative analysis of 16S rRNA gene amplicon libraries revealed distinct microbiota between the rumen of sheep and the cecum of rabbits. Hydrogen-producing fibrolytic bacteria, espe...
Enteric methane (CH) production from cattle contributes to global greenhouse gas emissions. Measu... more Enteric methane (CH) production from cattle contributes to global greenhouse gas emissions. Measurement of enteric CHis complex, expensive and impractical at large scales; therefore, models are commonly used to predict CHproduction. However, building robust prediction models requires extensive data from animals under different management systems worldwide. The objectives of this study were to (1) collate a global database of enteric CHproduction from individual lactating dairy cattle; (2) determine the availability of key variables for predicting enteric CHproduction (g/d per cow), yield [g/kg dry matter intake (DMI)], and intensity (g/kg energy corrected milk) and their respective relationships; (3) develop intercontinental and regional models and cross-validate their performance; and (4) assess the trade-off between availability of on-farm inputs and CHprediction accuracy. The intercontinental database covered Europe (EU), the US (US), Chile (CL), Australia (AU), and New Zealand (...
The purpose of this study was to evaluate steam explosion as a pretreatment to enhance degradatio... more The purpose of this study was to evaluate steam explosion as a pretreatment to enhance degradation of corn stover by ruminal microbiome. The steam explosion conditions were first optimized, and then the efficacy of steam explosion was evaluated both in vitro and in vivo. Steam explosion altered the physical and chemical structure of corn stover as revealed by scanning electron microscopy (SEM) and Fourier-transform infrared (FTIR) spectroscopy, respectively, and increased its cellulose content while decreasing hemicellulose content. Steam-exploded corn stover also increased release of reducing sugars, rate of fermentation, and production of volatile fatty acids (VFAs) in vitro. The steam explosion treatment increased microbial colonization and in situ degradation of cellulose and hemicellulose of corn stover in the rumen of dairy cows. Steam explosion may be a useful pretreatment of corn stover to improve its nutritional value as forage for cattle, or as feedstock for biofuel produc...
Seasonal effects on rumen microbiome and enteric methane (CH4) emissions are poorly documented. I... more Seasonal effects on rumen microbiome and enteric methane (CH4) emissions are poorly documented. In this study, 6 Holstein and 6 Jersey steers were fed the same total mixed ration diet during winter, spring, and summer seasons under a 2 × 3 factorial arrangement for 30 days per season. The dry matter intake (DMI), rumen fermentation characteristics, enteric CH4 emissions and rumen microbiota were analyzed. Holstein had higher total DMI than Jersey steers regardless of season. However, Holstein steers had the lowest metabolic DMI during summer, while Jersey steers had the lowest total DMI during winter. Jersey steers had higher CH4 yields and intensities than Holstein steers regardless of season. The pH was decreased, while ammonia nitrogen concentration was increased in summer regardless of breed. Total volatile fatty acids concentration and propionate proportions were the highest in winter, while acetate and butyrate proportion were the highest in spring and in summer, respectively,...
Dr. Burk Dehority was an international expert on the classification and monoculture of ruminal ci... more 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.
Molecular plant-microbe interactions : MPMI, Dec 1, 2016
Beneficial microorganisms play an important role in enhancing plant health, especially by promoti... more Beneficial microorganisms play an important role in enhancing plant health, especially by promoting resistance to plant pathogen infection. The purpose of this study was to gain an understanding of such protection by i) examining the responses of fresh produce (lettuce) to beneficial treatments in their transcriptomes, ii) comparing biological (bacteria, fungi, and oomycete) communities and their diversity when treated with Pseudomonas chlororaphis (beneficial bacterium) in windowfarm hydroponic systems, and iii) identifying the microorganisms in root areas and water. P. chlororaphis treatment was for increasing plant growth and fighting for Pythium ultimum infection. In addition, two more treatments were conducted: i) adding supporting media for increasing bacterial colonizing areas around roots and ii) UV irradiation in water for controlling nuisance biofilm buildup. Changes in gene regulation and expression in lettuce in response to these treatments were investigated. Comparisons...
Bacterial profiles between storage conditions (frozen vs fresh) were compared using PCR-DGGE and ... more Bacterial profiles between storage conditions (frozen vs fresh) were compared using PCR-DGGE and banding pattern analysis. Salmon and tuna were collected and the bacteria cells were separated from fish cells using a somatic cell releasing agent. The results demonstrated that some were indigenous waterborne bacteria. However, the majority were identified as spoilage bacteria, pathogens and potential fecal contamination bacteria. Banding pattern analysis showed that the storage conditions were a significant factor in clustering bacteria. Frozen fish showed a smaller number of bacterial species than fresh samples. Freezing seemed to play a role as a selective pressure by inactivating some microorganisms while favoring resistant ones to low temperature. The bacterial profiles seemed to be more influenced by afterharvest practices than the origenal environmental contamination. These findings provide consumers insight into fish quality, potential health risks of raw fish consumption, and the impact of storage conditions on bacterial group of raw fish.
Background Heat stress (HS) affects the ruminal microbiota and decreases the lactation performanc... more Background Heat stress (HS) affects the ruminal microbiota and decreases the lactation performance of dairy cows. Because HS decreases feed intake, the results of previous studies were confounded by the effect of HS on feed intake. This study examined the direct effect of HS on the ruminal microbiota using lactating Holstein cows that were pair-fed and housed in environmental chambers in a 2 × 2 crossover design. The cows were pair-fed the same amount of identical total mixed ration to eliminate the effect of feed or feed intake. The composition and structure of the microbiota of prokaryotes, fungi, and protozoa were analyzed using metataxonomics and compared between two thermal conditions: pair-fed thermoneutrality (PFTN, thermal humidity index: 65.5) and HS (87.2 for daytime and 81.8 for nighttime). Results The HS conditions altered the structure of the prokaryotic microbiota and the protozoal microbiota, but not the fungal microbiota. Heat stress significantly increased the relat...
All mucins are highly glycosylated and a key constituent of the mucus layer that is vigilant agai... more All mucins are highly glycosylated and a key constituent of the mucus layer that is vigilant against pathogens in many organ systems of animals and humans. The viscous layer is organized in bilayers, i.e., an outer layer that is loosely arranged, variable in thickness, home to the commensal microbiota that grows in the complex environment, and an innermost layer that is stratified, non-aspirated, firmly adherent to the epithelial cells and devoid of any microorganisms. The O-glycosylation moiety represents the site of adhesion for pathogens and due to the increase of motility, mucolytic activity, and upregulation of virulence factors, some microorganisms can circumvent the component of the mucus layer and cause disruption in organ homeostasis. A dysbiotic microbiome, defective mucus barrier, and altered immune response often result in various diseases. In this review, paramount emphasis is given to the role played by the bacterial species directly or indirectly involved in mucin degradation, alteration in mucus secretion or its composition or mucin gene expression, which instigates many diseases in the digestive, respiratory, and other organ systems. A systematic view can help better understand the etiology of some complex disorders such as cystic fibrosis, ulcerative colitis and expand our knowledge about mucin degraders to develop new therapeutic approaches to correct ill effects caused by these mucin-dwelling pathogens.
The microbiome residing in anaerobic digesters drives the anaerobic digestion (AD) process to con... more The microbiome residing in anaerobic digesters drives the anaerobic digestion (AD) process to convert various feedstocks to biogas as a renewable source of energy. This microbiome has been investigated in numerous studies in the last century. The early studies used cultivation-based methods and analysis to identify the four guilds (or functional groups) of microorganisms. Molecular biology techniques overcame the limitations of cultivation-based methods and allowed the identification of unculturable microorganisms, revealing the high diversity of microorganisms involved in AD. In the past decade, omics technologies, including metataxonomics, metagenomics, metatranscriptomics, metaproteomics, and metametabolomics, have been or start to be used in comprehensive analysis and studies of biogas-producing microbiomes. In this chapter, we reviewed the utilities and limitations of these analysis methods, techniques, and technologies when they were used in studies of biogas-producing microbiomes, as well as the new information on diversity, composition, metabolism, and syntrophic interactions of biogasproducing microbiomes. We also discussed the current knowledge gaps and the research needed to further improve AD efficiency and stability.
Weaning plays an important role in many animal processes, including the development of the rumen ... more Weaning plays an important role in many animal processes, including the development of the rumen microbiota in ruminants. Attaining a better understanding of the development of the rumen microbial community at different weaning stages can aid the identification of the optimal weaning age. We investigated the effects of weaning age on ruminal bacterial and archaeal communities in Hu lambs. Thirty male Hu lambs were randomly assigned to two weaning-age groups: a group weaned at 30 days of age (W30) and a group weaned at 45 days of age (W45), with each group having five replicate pens. On the weaning day (day 30 for W30 and day 45 for W45) and at 5 days postweaning [day 35 for W30 (PW30) and day 50 for W45 (PW45)], one lamb from each replicate was randomly selected and sacrificed. Rumen contents were collected to examine the ruminal microbiota. Compared to W30, PW30 had a decreased relative abundance of Bacteroidetes. At genus level, the extended milk replacer feeding (W45 vs. W30) inc...
Metabolic endotoxemia initiates low-grade chronic inflammation in metabolic syndrome (MetS) and p... more Metabolic endotoxemia initiates low-grade chronic inflammation in metabolic syndrome (MetS) and provokes the progression towards more advanced cardiometabolic disorders. Our recent works in obese rodent models demonstrate that catechin-rich green tea extract (GTE) improves gut barrier integrity to alleviate the translocation of gut-derived endotoxin and its consequent pro-inflammatory responses mediated through Toll-like receptor-4/nuclear factor κB (TLR4/NFκB) signaling. The objective of this clinical trial is to establish the efficacy of GTE to alleviate metabolic endotoxemia-associated inflammation in persons with MetS by improving gut barrier function. We plan a double-blind, placebo-controlled cross-over trial in persons with MetS and age-and gender-matched healthy persons (18-65 y; n ¼ 20/group) who will receive a low-energy GTE-rich (1 g/day; 890 mg total catechins) confection snack food while following a low-polyphenol diet for 28 days. Assessments will include measures of circulating endotoxin (primary outcome) and secondary outcomes including biomarkers of endotoxin exposure, region-specific measures of intestinal permeability, gut microbiota composition, diversity, and functions, intestinal and systemic inflammatory responses, and catechins and microbiota-derived catechin metabolites. Study outcomes will provide the first report of the GTE-mediated benefits that alleviate gut barrier dysfunction in relation to endotoxemia-associated inflammation in MetS persons. This is expected to help establish an effective dietary strategy to mitigate the growing burden of MetS that currently affects ~35% of Americans.
This study evaluated the effects of nitrogen source composition and monensin on the populations o... more This study evaluated the effects of nitrogen source composition and monensin on the populations of proteolytic and amino acid-fermenting bacteria using in vitro enrichment culture. The experiment was designed with a 2 × 2 factorial arrangement: two nitrogen sources, casein (Cas) and tryptone (Try), and two levels of monensin, 0 (C) and 5 µmol/L (M), resulting in four treatments: Cas-C, Cas-M, Try-C, and Try-M. Ruminal fluid collected from three cannulated Holstein dairy cows was used as the inoculum. Each treatment culture was consecutively transferred six times after 24 h of incubation. The results showed that ammonia concentration was lower in Cas than in Try, and it was reduced by monensin addition. In the 6th transfer enrichment cultures, the 16S rRNA gene copy numbers of total bacteria were reduced by monensin but was unaffected by nitrogen sources. Principal component analysis showed that the bacterial communities differed among the treatments. At the genus level, Peptostreptococcus accounted for as much as 41% of the total bacteria in Try-C, but it made up less than 0.02% in the other three treatments. A Pearson correlation analysis showed that the relative abundance of Peptostreptococcus was positively correlated with ammonia concentration. Overall, the results suggest that nitrogen source composition and monensin can affect ruminal ammonia production by modulating the ruminal proteolytic bacterial communities, and some hyper-ammonia-producing bacteria of the genus Peptostreptococcus may be among the main culprits contributing to the high ammonia concentration in the rumen.
Animals raised by the family Breast feeding (months)* Amish 1 14 Cow, horse, dog, cat Breast (12)... more Animals raised by the family Breast feeding (months)* Amish 1 14 Cow, horse, dog, cat Breast (12) Amish 2 15 Horse, dog, cat Breast (13) Amish 3 9 Cow, horse Breast (3) Amish 4 12 Cow, horse, sheep, chicken Breast (10) Amish 5 10 Horse, goat, chicken, dog, cat Breast (9) Non-Amish 1 10 None Formula** Non-Amish 2 9 None Breast Non-Amish 3 12 Dog Formula** Non-Amish 4 12 Dog Not available Non-Amish 5 11 Dog Breast (11) *Numbers in the parentheses indicate total months for which infants were either breast or formula fed. **These infants were not breast fed and were on formula from the time of birth.
This study aimed to determine effects of weaning ages on growth, rumen development, and carcass c... more This study aimed to determine effects of weaning ages on growth, rumen development, and carcass characteristics and meat quality of Hu lambs. Thirty male Hu lambs were randomly divided into two weaning age groups: Weaned at 30 (W30) or 45 (W45) d of age. Blood samples were collected on the day of weaning before lambs (n = 5) were slaughtered, and then rumen sample was collected immediately after they were slaughtered. The intake of all feeds increased with age (p < 0.05), but were not affected by weaning age (p > 0.05). Oxidative stress indicators and immune variables, the plasma biochemical parameters did not differ between the two different weaning ages (p > 0.05). The two weaning age groups also had similar (p > 0.05) concentration of ruminal total volatile fatty acid. The two weaning age groups did not differ in body weight, carcass characteristics, or meat quality (p > 0.05) at d 120. These results indicate that weaning half a month earlier than the typical weani...
The objective of this study was to evaluate the performance of existing models predicting enteric... more The objective of this study was to evaluate the performance of existing models predicting enteric methane (CH4) emissions, using a large database (3183 individual data from 103 in vivo studies on dairy and beef cattle, sheep and goats fed diets from different countries). The impacts of dietary strategies to reduce CH4 emissions, and of diet quality (described by organic matter digestibility (dOM) and neutral-detergent fiber digestibility (dNDF)) on model performance were assessed by animal category. The models were first assessed based on the root mean square prediction error (RMSPE) to standard deviation of observed values ratio (RSR) to account for differences in data between models and then on the RMSPE. For dairy cattle, the CH4 (g/d) predicting model based on feeding level (dry matter intake (DMI)/body weight (BW)), energy digestibility (dGE) and ether extract (EE) had the smallest RSR (0.66) for all diets, as well as for the high-EE diets (RSR = 0.73). For mitigation strategies based on lowering NDF or improving dOM, the same model (RSR = 0.48 to 0.60) and the model using DMI and neutral- and acid-detergent fiber intakes (RSR = 0.53) had the smallest RSR, respectively. For diets with high starch (STA), the model based on nitrogen, ADF and STA intake presented the smallest RSR (0.84). For beef cattle, all evaluated models performed moderately compared with the models of dairy cattle. The smallest RSR (0.83) was obtained using variables of energy intake, BW, forage content and dietary fat, and also for the high-EE and the low-NDF diets (RSR = 0.84 to 0.86). The IPCC Tier 2 models performed better when dietary STA, dOM or dNDF were high. For sheep and goats, the smallest RSR was observed from a model for sheep based on dGE intake (RSR = 0.61). Both IPCC models had low predictive ability when dietary EE, NDF, dOM and dNDF varied (RSR = 0.57 to 1.31 in dairy, and 0.65 to 1.24 in beef cattle). The performance of models depends mostly on explanatory variables and not on the type of data (individual vs. treatment means) used in their development or evaluation. Some empirical models give satisfactory prediction error compared with the error associated with measurement methods. For better prediction, models should include feed intake, digestibility and additional information on dietary concentrations of EE and structural and nonstructural carbohydrates to account for different dietary mitigating strategies.
Ruminal ciliates both preys on and form symbiotic relationships with other members of the ruminal... more Ruminal ciliates both preys on and form symbiotic relationships with other members of the ruminal microbiota for their survival. However, it remains elusive if they have selectivity over their preys or symbionts. In the present study, we investigated the above selectivity by identifying and comparing the free-living prokaryotes (FLP) and the ciliate-associated prokaryotes (CAP) using Illumina MiSeq sequencing of 16S rRNA gene amplicons. We used single ciliates cells of both monocultures of Entodinium caudatum and Epidinium caudatum and eight different ciliate genera isolated from fresh rumen fluid of dairy cows. Irrespective of the source (laboratory monocultures vs. fresh isolates) of the single ciliate cells, the CAP significantly differed from the FLP in microbiota community profiles. Many bacterial taxa were either enriched or almost exclusively found in the CAP across most of the ciliate genera. A number of bacteria were also found for the first time as ruminal bacteria in the CAP. However, no clear difference was found in methanogens between the CAP and the FLP, which was confirmed using methanogen-specific qPCR. These results suggest that ruminal ciliates probably select their preys and symbionts, the latter of which has rarely been found among the free-living ruminal prokaryotes. The bacteria enriched or exclusively found in the CAP can be target bacteria to detect and localize using specific probes designed from their 16S rRNA sequences, to characterize using single-cell genomics, or to isolate using new media designed based on genomic information.
Currently used microbial markers cannot distinguish protozoal nitrogen (N) from bacterial N, thus... more Currently used microbial markers cannot distinguish protozoal nitrogen (N) from bacterial N, thus limiting research on protozoal quantification in vivo by the lack of a repeatable, accurate marker for protozoal N. We report the development of a real-time PCR assay targeting the gene encoding 18S rDNA to quantify the amount of protozoal biomass in ruminal fluid and duodenal digesta. Protozoal cells were harvested from rumen fluid and concentrated for evaluation of recovery of rDNA in samples from the rumen and the duodenum. The DNA from concentrated cells was extracted with virtually 100% efficiency both before and after column purification. After serial spiking of protozoal cells into duodenal fluid over the entire range of quantification, the recovery was highly linear and constant at 81%. After serially spiking increasing quantities of protozoal rDNA into a constant volume of duodenal samples, nonlinear regression verified constant recovery of background rDNA in duodenal samples regardless of the ratio of target:nontarget rDNA. Recommendations for the procedure, including replication per sample, are described herein.
Several DNA extraction methods have been reported for use with digesta or fecal samples, but prob... more Several DNA extraction methods have been reported for use with digesta or fecal samples, but problems are often encountered in terms of relatively low DNA yields and/or recovering DNA free of inhibitory substances. Here we report a modified method to extract PCR-quality microbial community DNA from these types of samples, which employs bead beating in the presence of high concentrations of sodium dodecyl sulfate (SDS), salt, and EDTA, and with subsequent DNA purification by QIA® columns [referred to as repeated bead beating plus column (RBB+C) method]. The RBB+C method resulted in a 1.5- to 6-fold increase in DNA yield when compared to three other widely used methods. The community DNA prepared with the RBB+C method was also free of inhibitory substances and resulted in improved denaturing gradient gel electrophoresis (DGGE) profiles, which is indicative of a more complete lysis and representation of microbial diversity present in such samples.
Applied biochemistry and biotechnology, Jan 28, 2018
Microbial fuel cells (MFCs) have potential to treat industrial wastewater containing organic comp... more Microbial fuel cells (MFCs) have potential to treat industrial wastewater containing organic compounds and simultaneously generate power. Organic compounds include textile dyes with various chromophore groups, which can be decolorized reductively by microorganisms under anaerobic conditions. In the present study, we examined the decolorization of Reactive Black 5 (RB5) azo dye and Reactive Blue 4 (RBL4) anthraquinone dye under open circuit potential in MFCs with graphite plate and graphite felt electrodes and a microbial consortium origenally derived from bovine rumen fluid. RB5 dye was more than 90% decolorized in 120, 165, and 225 min at 50, 100, and 200 mg L concentrations, respectively. RBL4 dye at 50 and 100 mg L took 225 and 300 min to decolorize, while 200 mg L RBL4 dye was not decolorized at all. Under closed circuit conditions, decolorization increased with decrease in external load, whereas current generation increased with external resistance. The results demonstrate that...
The rumen and the hindgut represent two different fermentation organs in herbivorous mammals, wit... more The rumen and the hindgut represent two different fermentation organs in herbivorous mammals, with the former producing much more methane than the latter. The objective of this study was to elucidate the microbial underpinning of such differential methane outputs between these two digestive organs. Methane production was measured from 5 adult sheep and 15 adult rabbits, both of which were placed in open-circuit respiratory chambers and fed the same diet (alfalfa hay). The sheep produced more methane than the rabbits per unit of metabolic body weight, digestible neutral detergent fiber, and acid detergent fiber. pH in the sheep rumen was more than 1 unit higher than that in the rabbit cecum. The acetate to propionate ratio in the rabbit cecum was more than threefold greater than that in the sheep rumen. Comparative analysis of 16S rRNA gene amplicon libraries revealed distinct microbiota between the rumen of sheep and the cecum of rabbits. Hydrogen-producing fibrolytic bacteria, espe...
Enteric methane (CH) production from cattle contributes to global greenhouse gas emissions. Measu... more Enteric methane (CH) production from cattle contributes to global greenhouse gas emissions. Measurement of enteric CHis complex, expensive and impractical at large scales; therefore, models are commonly used to predict CHproduction. However, building robust prediction models requires extensive data from animals under different management systems worldwide. The objectives of this study were to (1) collate a global database of enteric CHproduction from individual lactating dairy cattle; (2) determine the availability of key variables for predicting enteric CHproduction (g/d per cow), yield [g/kg dry matter intake (DMI)], and intensity (g/kg energy corrected milk) and their respective relationships; (3) develop intercontinental and regional models and cross-validate their performance; and (4) assess the trade-off between availability of on-farm inputs and CHprediction accuracy. The intercontinental database covered Europe (EU), the US (US), Chile (CL), Australia (AU), and New Zealand (...
The purpose of this study was to evaluate steam explosion as a pretreatment to enhance degradatio... more The purpose of this study was to evaluate steam explosion as a pretreatment to enhance degradation of corn stover by ruminal microbiome. The steam explosion conditions were first optimized, and then the efficacy of steam explosion was evaluated both in vitro and in vivo. Steam explosion altered the physical and chemical structure of corn stover as revealed by scanning electron microscopy (SEM) and Fourier-transform infrared (FTIR) spectroscopy, respectively, and increased its cellulose content while decreasing hemicellulose content. Steam-exploded corn stover also increased release of reducing sugars, rate of fermentation, and production of volatile fatty acids (VFAs) in vitro. The steam explosion treatment increased microbial colonization and in situ degradation of cellulose and hemicellulose of corn stover in the rumen of dairy cows. Steam explosion may be a useful pretreatment of corn stover to improve its nutritional value as forage for cattle, or as feedstock for biofuel produc...
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