Solid-associated Bacteria Research Articles

Megasphaera elsdenii and Saccharomyces cerevisiae as direct fed microbials and their impact on ruminal microbiome during an acute acidosis challenge in continuous culture.

Our objective was to evaluate the effects of combinations of Saccharomyces cerevisiae and Megasphaera elsdenii as direct-fed microbials (DFM) on ruminal microbiome during an acute acidosis challenge in a continuous culture system. Treatments provided a DFM dose of 1 × 108 colony-forming unit (CFU)/mL, as follows: control (no DFM), YM1 (S. cerevisiae and M. elsdenii strain 1), YM2 (S. cerevisiae and M. elsdenii strain 2), and YMM (S. cerevisiae and half of the doses of M. elsdenii strains 1 and 2). We conducted four experimental periods of 11 d, which consisted of non-acidotic days (1 to 8) and acidotic challenge days (9 to 11) to establish acute ruminal acidosis conditions with a common basal diet containing 12% neutral detergent fiber and 58% starch. Treatments were applied from days 8 to 11, and samples of liquid and solid-associated bacteria were collected on days 9 to 11. Overall, 128 samples were analyzed by amplification of the V4 region of bacterial 16S rRNA, and data were analyzed with R and SAS for alpha and beta diversity, taxa relative abundance, and correlation of taxa abundance with propionate molar proportion. We observed a lower bacterial diversity (Shannon index, P = 0.02) when YM1 was added to the diet in comparison to the three other treatments. Moreover, compared to control, addition of YM1 to the diet increased relative abundance of phylum Proteobacteria (P = 0.05) and family Succinivibrioceae (P = 0.05) in the solid fraction and tended to increase abundance of family Succinivibrioceae (P = 0.10) and genus Succinivibrio (P = 0.09) in the liquid fraction. Correlation analysis indicated a positive association between propionate molar proportion and relative abundance of Proteobacteria (r = 0.36, P = 0.04) and Succinivibrioceae (r = 0.36, P = 0.05) in the solid fraction. The inclusion of YM1 in high-grain diets with a high starch content resulted in greater abundance of bacteria involved in succinate synthesis which may have provided the substrate for the greater propionate synthesis observed.

Changes in the Fermentation and Bacterial Community by Artificial Saliva pH in RUSITEC System.

The purpose of the study was to assess the artificial saliva (AS) pH on ruminal fermentation and rumen bacteria community in the rumen simulation technique (RUSITEC) system. The experiment was performed in two treatments (low AS pH vs. high AS pH) with four replicates. The low AS pH was sustained by altering the composition of the AS (NaHCO3 from 9.8 to 1.96 g/L, Na2HPO4 from 9.3 to 1.86 g/L) according to McDougall's method. The diets were supplemented with 16 g basic diets with forage to the concentrate ratio of 50:50. The experiments were conducted over 13-day incubation periods, with 9 days adaption and 4 days sample collection. The results showed low AS pH decreased dry matter (DM) degradability (64.37 vs. 58.67%), organic matter (OM) degradability (64.38 vs. 59.32%), neutral detergent fiber (NDF) degradability (46.87 vs. 39.94%), acid detergent fiber (ADF) degradability (38.16 vs. 31.13%), and crude protein (CP) degradability (70.33 vs. 62.99%), respectively. Compared with the high AS pH, the low AS pH increased the proportion of butyrate (P = 0.008) and decreased the proportion of propionate (P < 0.001). At the bacteria community, the low AS pH increased the abundances of Spirochaetes (P = 0.001) and Synergistetes (P = 0.004) and decreased the Verrucomicrobia abundance (P = 0.004) in solid-associated bacteria. At the genus level, the low AS pH increased the abundance of Lactobacillus (P = 0.050) and decreased the abundance of Schwartzia (P = 0.002) in solid-associated bacteria. The abundances of Prevotellaceae_YAB2003_group (P = 0.040), Schwartzia (P = 0.002), and Ruminobacter (P = 0.043) were lower in the low AS pH group compared with the high AS pH group in liquid-associated bacteria. Low AS pH decreased the number of Ruminococcus albus, Ruminococcus flavefaciens, Fibrobacter succinogenes (P < 0.001) both in the solid- and liquid-associated bacteria, respectively. The results of the present study included three groups of bacteria communities according to the different sensitives to rumen pH: the abundances of Lactobacillus, Succinivibrio, and Prevotella_7 are increased with decreasing AS pH; the amounts of R. albus, R. flavefaciens, F. succinogenes as well as the abundances of Schwartzia and Ruminobacter decreased with the reducing AS pH; the abundances of Selenomonas_1, Rikenellaceae_RC9_gut_group, and Succiniclasticum were not affected by the AS pH in RUSTITEC.

PacBio and Illumina MiSeq Amplicon Sequencing Confirm Full Recovery of the Bacterial Community After Subacute Ruminal Acidosis Challenge in the RUSITEC System

The impact of subacute rumen acidosis (SARA) on the rumen bacterial community has been frequently studied in in vivo trials. Here we investigated whether these alterations can be mirrored by using the rumen simulation technique (RUSITEC) as an in vitro model for this disease. We hypothezised that the bacterial community fully recovers after a subacute ruminal acidosis challenge. We combined a PacBio nearly full-length 16S rRNA gene analysis with 16S rRNA gene Illumina MiSeq sequencing of the V4 hypervariable region. With this hybrid approach, we aimed to get an increased taxonomic resolution of the most abundant bacterial groups and an overview of the total bacterial diversity. The experiment consisted of a control period I and a SARA challenge and ended after a control period II, of which each period lasted 5 d. Subacute acidosis was induced by applying two buffer solutions, which were reduced in their buffering capacity (SARA buffers) during the SARA challenge. Two control groups were constantly infused with the standard buffer solution. Furthermore, the two SARA buffers were combined with three different feeding variations, which differed in their concentrate-to-hay ratio. The induction of SARA led to a decrease in pH below 5.8, which then turned into a steady-state SARA. Decreasing pH values led to a reduction in bacterial diversity and richness. Moreover, the diversity of solid-associated bacteria was lower for high concentrate groups throughout all experimental periods. Generally, Firmicutes and Bacteroidetes were the predominant phyla in the solid and the liquid phase. During the SARA period, we observed a decrease in fibrolytic bacteria although lactate-producing and -utilizing families increased in certain treatment groups. The genera Lactobacillus and Prevotella dominated during the SARA period. With induction of the second control period, most bacterial groups regained their initial abundance. In conclusion, this in vitro model displayed typical bacterial alterations related to SARA and is capable of recovery from bouts of SARA. Therefore, this model can be used to mimic SARA under laboratory conditions and may contribute to a reduction in animal experiments.

Ruminal use of undegraded-feed soluble protein and accuracy of the estimations of the nutrient content in ruminal bacteria.

The possible escape from the rumen of undegraded-feed soluble proteins (SP) was investigated using nitrogen-15 (15 N) infusions (25 mg) in three rumen and duodenum cannulated wethers. Animals were fed three isoproteic diets differing in SP content and including protein concentrates either untreated (control) or treated with solutions of either malic acid (MHT) or orthophosphoric acid (OHT) and heat. Compared with control, MHT and OHT diets reduced ruminal concentrations of ammonia-nitrogen (NH3 -N) by 35.9% (P = 0.007), non-ammonia nitrogen (NAN) by 36.8% (P = 0.007), and SP-nitrogen (SP-N) by 45.2% (P = 0.072) over the post-feeding period. Both NAN and SP-N were lower (P ≤ 0.040) for OHT than for MHT diet. The 15 N enrichment of NAN and SP-N did not vary either among diets or with time, and both values were closely related (R2 = 0.965; P < 0.001). Estimations, either using solid-associated bacteria (SAB) or liquid-associated bacteria (LAB) as a reference, indicated that 0.983 and 0.894 of SP-N (values averaged across diets) was of microbial origin, respectively, which would indicate a practically negligible ruminal escape of feed SP-N. Values of 15 N-enrichment in SAB and LAB fitted well to previously published SAB-LAB relationships, indicating a 22% underevaluation of the N supply from SAB when only LAB is used as a reference. Both the negligible ruminal escape of feed SP and the underevaluation of the bacterial nutrient supply as a consequence of the use of LAB as the only bacterial reference should be considered to improve ruminant protein feeding systems. © 2019 Society of Chemical Industry.

Comparison of automated ribosomal intergenic spacer analysis (ARISA) and denaturing gradient gel electrophoresis (DGGE) techniques for analysing the influence of diet on ruminal bacterial diversity

ABSTRACTThe objective of this study was to compare the automated ribosomal intergenic spacer analysis (ARISA) and the denaturing gradient gel electrophoresis (DGGE) techniques for analysing the effects of diet on diversity in bacterial pellets isolated from the liquid (liquid-associated bacteria (LAB)) and solid (solid-associated bacteria (SAB)) phase of the rumen. The four experimental diets contained forage to concentrate ratios of 70:30 or 30:70 and had either alfalfa hay or grass hay as forage. Four rumen-fistulated animals (two sheep and two goats) received the diets in a Latin square design. Bacterial pellets (LAB and SAB) were isolated at 2 h post-feeding for DNA extraction and analysed by ARISA and DGGE. The number of peaks in individual samples ranged from 48 to 99 for LAB and from 41 to 95 for SAB with ARISA, and values of DGGE-bands ranged from 27 to 50 for LAB and from 18 to 45 for SAB. The LAB samples from high concentrate-fed animals tended (p < 0.10) to show greater peak numbers and Shannon index values than those isolated from high forage-fed animals with ARISA, but no differences were identified with DGGE. The SAB samples from high concentrate-fed animals had lower (p < 0.05) peak numbers and Shannon index values than those from animals fed high-forage diets with ARISA, but only a trend was noticed for these parameters with DGGE (p < 0.10). The ARISA detected that animals fed alfalfa hay diets showed lower (p < 0.05) SAB diversity than those fed grass hay diets, but no differences were observed with DGGE. No effect of forage type on LAB diversity was detected by any technique. In this study, ARISA detected some changes in ruminal bacterial communities that were not detected by DGGE, and therefore ARISA was considered more appropriate for assessing bacterial diversity of ruminal bacterial pellets. The results highlight the impact of the fingerprinting technique used to draw conclusions on dietary factors affecting bacterial diversity in ruminal bacterial pellets.

A Systems Biology Approach Reveals Differences in the Dynamics of Colonization and Degradation of Grass vs. Hay by Rumen Microbes with Minor Effects of Vitamin E Supplementation.

Increasing the efficiency of utilization of fresh and preserved forage is a key target for ruminant science. Vitamin E is often used as additive to improve product quality but its impact of the rumen function is unknown. This study investigated the successional microbial colonization of ryegrass (GRA) vs. ryegrass hay (HAY) in presence of zero or 50 IU/d supplementary vitamin E, using a rumen simulation technique. A holistic approach was used to link the dynamics of feed degradation with the structure of the liquid-associated (LAB) and solid-associated bacteria (SAB). Results showed that forage colonization by SAB was a tri-phasic process highly affected by the forage conservation method: Early colonization (0–2 h after feeding) by rumen microbes was 2× faster for GRA than HAY diets and dominated by Lactobacillus and Prevotella which promoted increased levels of lactate (+56%) and ammonia (+18%). HAY diets had lower DM degradation (-72%) during this interval being Streptococcus particularly abundant. During secondary colonization (4–8 h) the SAB community increased in size and decreased in diversity as the secondary colonizers took over (Pseudobutyrivibrio) promoting the biggest differences in the metabolomics profile between diets. Secondary colonization was 3× slower for HAY vs. GRA diets, but this delay was compensated by a greater bacterial diversity (+197 OTUs) and network complexity resulting in similar feed degradations. Tertiary colonization (>8 h) consisted of a slowdown in the colonization process and simplification of the bacterial network. This slowdown was less evident for HAY diets which had higher levels of tertiary colonizers (Butyrivibrio and Ruminococcus) and may explain the higher DM degradation (+52%) during this interval. The LAB community was particularly active during the early fermentation of GRA and during the late fermentation for HAY diets indicating that the availability of nutrients in the liquid phase reflects the dynamics of feed degradation. Vitamin E supplementation had minor effects but promoted a simplification of the LAB community and a slight acceleration in the SAB colonization sequence which could explain the higher DM degradation during the secondary colonization. Our findings suggest that when possible, grass should be fed instead of hay, in order to accelerate feed utilization by rumen microbes.

Effect of Quebracho Tannin Extract on Soybean and Linseed Oil Biohydrogenation by Solid Associated Bacteria: An in vitro Study

An in vitro trial was carried out to study the effects of Quebracho tannins extract (QE) on fatty acid profile of rumen solid adherent bacteria (SAB) during the fermentation of diets supplemented with soybean or linseed oil, as sources of linoleic (LA; 18:2 n-6) and α-linolenic acid (α-LNA; 18:3 n-3), respectively. Two control diets were prepared using a basal mixture of grass hay [760 g/kg on dry matter (DM)], soybean meal (55 g/kg DM), barley meal (130 g/kg DM), vitamin mineral premix (20 g/kg DM) and 35 g/kg DM of soybean (SOC diet) or linseed oil (LOC diet) as lipid supplement. Other two diets (SOCT and LOCT) were obtained by integrating SOC and LOC with QE (49 g/kg DM). The results confirmed that Quebracho tannins may be an effective method for reducing in SAB the biohydrogenation of LA (17.3 vs 34.5 g/100 g of fatty acid in SOC and SOCT, respectively) and LNA (10.7 vs 21.4 g/100 g of fatty acid in LOC and LOCT, respectively), but not for increasing the rumen accumulation of cis9, trans11 18:2 (0.77 vs 0.32 g/100 g of fatty acid in SOC and SOCT, respec tively; 0.51 vs 0.43 g/100 g of fatty acid in LOC and LOCT, respectively) and trans11 18:1 (6.15 vs 3.64 g/100 g of fatty acid in SOC and SOCT, respectively; 5.53 vs 4.47 g/100 g of fatty acid in LOC and LOCT, respectively).

Impact of subacute ruminal acidosis on the diversity of liquid and solid-associated bacteria in the rumen of goats

This study was aimed to investigate the impact of subacute ruminal acidosis (SARA) on the diversity of liquid (LAB) and solid-associated bacteria (SAB) following high-grain feeding. Six ruminally cannulated goats were divided into two groups: one group was fed a hay diet (COD), and the other group was fed a high grain diet (SAID). Rumen liquids and rumen solids were sampled after 2 weeks adaption. SARA was diagnosed with a pH below 5.8 for 8 h. SAID decreased ruminal pH (P < 0.001) and increased the acetate (P = 0.017), propionate (P = 0.001), butyrate (P < 0.001) and total volatile fatty acid (P < 0.001) concentration in rumen compared with the COD. Denaturing gradient gel electrophoresis fingerprints analysis revealed a clear separation between both the diet and the fraction of rumen digesta in bacterial communities. Pyrosequencing analysis showed that the proportion of phylum Bacteroidetes in the SAID-LAB and SAID-SAB communities was less than in the COD group, whereas the SAID group had a greater percentage of Firmicutes in both the LAB and SAB libraries. UniFrac analyses and a Venn diagram revealed a large difference between the two diets in the diversity of rumen bacterial communities. Overall, our findings revealed that SARA feeding did alter the community structure of rumen liquids and rumen solids. Thus, manipulation of dietary factors, such as ratio of forage to concentrate may have the potential to alter the microbial composition of rumen liquid and rumen solid.

Technical note: Fatty acids and purine profile of cecum and colon bacteria as indicators of equine microbial metabolism1

The potential use of odd- and branched-chain fatty acids (OBCFA) and purine bases (PB) as microbial markers in the equine hindgut was studied. For this purpose, feed particles adherent bacteria [solid associated bacteria (SAB)] and planktonic bacteria [liquid associated bacteria (PAB)] were isolated from total cecum and colon contents of 8 healthy, crossbred horses (9 ± 3 yr). Horses were fasted for 12 to 15 h before slaughter, and the cecum and colon were identified and clamped in their extremities to avoid mixing of digesta contents. The total cecum or colon contents was collected into thermal containers previously filled with CO2, immediately transported to the laboratory, and subjected to separation of solid and liquid phases to obtain bacterial PAB and SAB pellets from each horse. Overall differences observed were mainly between site of bacterial collection (cecum vs. colon) rather than between type of bacterial population (PAB vs. SAB). Cecal bacteria fraction had greater (P < 0.05) OM, PB, and branched-chain fatty acids (BCFA):odd-chain fatty acids (OFA) ratio but less (P < 0.05) BCFA, OFA, BCFA:PB ratio, and adenine:guanine ratio than colon bacterial biomass. Results indicated that the composition of cecal and colon bacteria is very different from that of similar ecosystems (e.g., rumen). These differences can be a reflection of different growth stages or nutrition of particular populations as well as different bacterial metabolic activities. Results presented herein provide evidence that PB and fatty acids can be used as microbial markers in equine studies.

Use of a colon simulation technique to assess the effect of live yeast on fermentation parameters and microbiota of the colon of pig

The impact of 2 doses of a Saccharomyces cerevisiae were evaluated, 5 × 10(10) cfu/kg of feed (L1) and 5 × 10(11) cfu/kg of feed (L2) against a control (CON) with no added yeast, using an in vitro model [colon simulation technique (Cositec)] to mimic digestion in the pig colon. The L2 (but not L1) dose significantly improved DM digestibility compared to CON (61 v 58%) and increased NH(3) concentrations (+15%). Volatile fatty acid concentrations increased with L2 compared to CON--isobutyrate (+13.5%), propionate (+8.5%), isovalerate (+17.8%), and valerate (+25%)--but only valerate was increased with L1 (+14.2%). The analysis of microbiota from the liquid associated bacteria (LAB) and solid associated bacteria (SAB) revealed an interaction between the fraction and treatment (P < 0.05). Indeed, L2 had a significant impact on SAB and LAB (P < 0.01) whereas L1 only tended to change the structure of the population in the SAB (P < 0.1). Overall, this study showed that a live yeast probiotic could improve digestion in a colonic simulation model but only at the higher dose used and this effect was associated with a shift in the bacterial population therein.

Effects of dietary non-ionic surfactant and forage to concentrate ratio on bacterial population and fatty acid composition of rumen bacteria and plasma of goats

This study was conducted to investigate effects of alkyl polyglycoside (APG) in diets that varied in forage to concentrate ratio (F:C) on ruminal microbial and plasma fatty acid (FA) composition and bacterial population in goats. A 2×2 factorial experiment was arranged within a 4×4 Latin square design using four wether goats fitted with permanent ruminal fistulae. Treatments included two levels of dietary F:C (40:60 vs. 60:40, on an air dry basis) and APG (no APG vs. 6.5g APG per day per animal). Dietary APG inclusion increased the proportion of iso-14:0 (P=0.03), and decreased the proportions of anteiso-17:0 (P=0.04) and monounsaturated fatty acids (MUFA) (P=0.04) in solid associated bacteria (SAB), but had no effect on FA in liquid associated bacteria (LAB) or in plasma. In addition, APG decreased (P<0.05) the Ruminococcus albus population. The major effects of APG were independent of F:C ratio. High dietary F:C decreased the proportions of 17:0 (P=0.01) and 9c12c18:2 (P=0.05) in LAB, decreased iso-13:0 (P=0.04) in SAB and 9c12c18:2 (P=0.05) in plasma, increased the proportions of anteiso-13:0 (P=0.04) in LAB, and 17:0 (P=0.0003) and 9c18:1 (P=0.03) in plasma, but had no effect on the ruminal bacterial population. These results indicate that, in both low and high F:C diets, dietary APG alter the FA composition of ruminal bacteria, which further imply a change in function and survival of rumen bacteria.

Composition of free and adherent ruminal bacteria: inaccuracy of the microbial nutrient supply estimates obtained using free bacteria as reference samples and 15N as the marker

Previous studies have indicated that 15N enrichment of solid-associated bacteria (SAB) may be predicted from the same value in liquid-associated bacteria (LAB). The aims of this study were to confirm this and to measure the error in the nutrient supply from SAB, when LAB are used as the reference sample. For this purpose, the chemical and amino acid (AA) compositions of both the bacterial populations were studied in four experiments carried out on different groups of three rumen cannulated wethers. Diets (one in Experiments 1 and 4 and three in Experiments 2 and 3) had forage-to-concentrate ratios (dry matter (DM) basis) between 2 : 1 and 40 : 60, and were consumed at intake levels between 40 and 75 g DM/kg (BW)0.75. The bacteria samples were isolated after continuous infusion of (15NH4)2SO4 (40, 18, 30 and 25 mg 15N/day, in Experiments 1 to 4, respectively) for at least 14 days. In all experiments, SAB had consistently higher concentrations of organic matter (826 v. 716 g/kg DM, as average) and total lipids (192 v. 95 g/kg DM, as average) than LAB. Similar CP concentrations of both populations were observed, except a higher concentration in SAB than in LAB in Experiment 3. A consistent (in Experiment 4 only as tendency) higher AA-N/total N ratio (on average 17.5%) was observed in SAB than in LAB. The 15N enrichment in SAB was systematically lower than in LAB. On the basis of the results of all studies a close relationship was found between the 15N enrichment in SAB and LAB, which was shown irrespective of experiments. This relationship was established from Experiments 1 and 2 and the above cited previous results (n = 20; P < 0.001; R2 = 0.996), and then confirmed from the results of Experiments 3 and 4. These relationships between SAB and LAB demonstrate that CP supply from SAB is underevaluated by, on average, 21.2% when LAB are used as the reference. This underevaluation was higher for true protein and even higher for the lipid supply (32.5% and 59.6%, respectively, as an average of the four experiments). Large differences in AA profile were observed between SAB and LAB. The prediction equation obtained using 15N as the marker may be used to correct the errors associated with the traditional use of LAB as the reference sample, and therefore to obtain more accurate estimates of the microbial nutrient supply to the ruminants.

Study of the effect of presence or absence of protozoa on rumen fermentation and microbial protein contribution to the chyme1

The aim of this study was to investigate the effect of presence or absence of protozoa on rumen fermentation and efficiency of microbial protein synthesis under different diets. Of 20 twin paired lambs, 1 lamb of each pair was isolated from the ewe within 24 h after birth and reared in a protozoa-free environment (n = 10), whereas their respective twin-siblings remained with the ewe (faunated, n = 10). When lambs reached 6 mo of age, 5 animals of each group were randomly allocated to 1 of 2 experimental diets consisting of either alfalfa hay as the sole diet, or 50:50 mixed with ground barley grain according to a 2 × 2 factorial arrangement of treatments. After 15 d of adaptation to the diet, the animals were euthanized and total rumen and abomasal contents were sampled to estimate rumen microbial synthesis using C(31) alkane as flow marker. Different ((15)N and purine bases) and a novel (recombinant DNA sequences) microbial markers, combined with several microbial reference extracts (rumen protozoa, liquid and solid associated bacteria) were evaluated. Absence of rumen protozoa modified the rumen fermentation pattern and decreased total tract OM and NDF digestibility in 2.0 and 5.1 percentage points, respectively. The effect of defaunation on microbial N flow was weak, however, and was dependent on the microbial marker and microbial reference extract considered. Faunated lambs fed with mixed diet showed the greatest rumen protozoal concentration and the least efficient microbial protein synthesis (29% less than the other treatments), whereas protozoa-free lambs fed with mixed diet presented the smallest ammonia concentration and 34% greater efficiency of N utilization than the other treatments. Although (15)N gave the most precise estimates of microbial synthesis, the use of recombinant DNA sequences represents an alternative that allows separate quantification of the bacteria and protozoa contributions. This marker showed that presence of protozoa decrease the bacterial-N flow through the abomasum by 33%, whereas the protozoa-N contribution to the microbial N flow increased from 1.9 to 14.1% when barley grain was added to the alfalfa hay. Absolute data related to intestinal flow must be treated with caution because the limitations of the sampling and maker system employed.

Effects of alkyl polyglycoside, a nonionic surfactant, and forage-to-concentrate ratio on rumen fermentation, amino acid composition of rumen content, bacteria and plasma in goats

In the present study, the effects of different forage-to-concentrate ratios (F:C) and an alkyl polyglycoside (APG) supplementation on parameters of rumen and blood metabolism were investigated in goats. A 2 × 2 factorial experiment was arranged within a 4 × 4 Latin square design (four 22-day periods), using four wether goats equipped with permanent ruminal cannulas. The experimental diets included two F:C levels (40:60 vs. 60:40), and two APG supplementation levels (None or 13 ml APG daily per animal). Rumen contents and blood samples were collected at the end of each period. Dietary F:C alteration affected plasma urea and influenced the proportions of leucine, histidine, arginine, glycine, proline, alanine, valine, phenylalanine, cysteine and tyrosine in rumen content, and the proportions of methionine, threonine and proline in solid-associated bacteria (SAB) significantly. Dietary APG decreased the proportions of valine and phenylalanine in rumen content, and the histidine content of liquid-associated bacteria. The interaction between dietary F:C and APG was significant for the proportions of glycine and alanine in rumen content, and the proportions of lysine and threonine in SAB. The proportion of lysine was greater, but the proportion of threonine was less in SAB for goats fed high F:C diet without APG supplementation. The proportions of plasma free amino acids and glucose concentration were not affected by experimental treatments. These results indicated that dietary APG addition affected the amino acid composition of the rumen content and ruminal bacteria, but this depended on the dietary F:C ratio. It is necessary to validate the effectiveness of dietary APG supplementation in further studies with more animals.

Effect of chestnut and quebracho tannins on fatty acid profile in rumen liquid- and solid-associated bacteria: an in vitro study

Tannins are phenolic compounds that interfere with biohydrogenation (BH) of polyunsaturated fatty acids (FAs). The aim of the present in vitro study was to investigate the effects of two different sources of tannins on FA profiles of rumen bacteria, with particular reference to rumenic and vaccenic acid. A control diet (C; composed of 300 g/kg of wheat straw, 132 g/kg of soyabean meal, 96 g/kg of barley meal, 152 g/kg of maize meal, 300 g/kg of maize gluten and 20 g/kg of mineral vitamin premix, all expressed on dry matter (DM)) and four diets, obtained by adding to C two different types of tannins from chestnut (TC) and from quebracho (TQ) at two concentration levels (49 and 82 g/kg DM), were compared. The content of the main unsaturated FAs (C18:1 cis9, C18:1 trans11, C18:2 cis9, cis12 and C18:3 cis9, cis12, cis15) from solid-associated bacteria (SAB) and liquid-associated bacteria (LAB) was affected by the presence of tannins in the diets. In particular, C18:1 trans11 content was significantly increased, especially with TC1, whereas the decreasing of C18:1 cis9 was unaffected, regardless of the presence or the kind of tannins added to feeds. SAB contained higher amounts of intermediates of polyunsaturated FA BH (as C18:1 trans11 and C18:2 cis9, trans11) than LAB that were characterized by a higher amount of C18:0. In the concentration range adopted in this study, the effect of TC and TQ on changes of bacterial FA profile was comparable. Tannins seem to be a good means to modulate the FA profile of rumen bacteria, favouring the accumulation of C18:1 trans11 during in vitro rumen fermentation.

Comparison of fermentation of diets of variable composition and microbial populations in the rumen of sheep and Rusitec fermenters. II. Protozoa population and diversity of bacterial communities

Four ruminally and duodenally cannulated sheep and 8 Rusitec fermenters were used to determine the effects of dietary characteristics on microbial populations and bacterial diversity. The purpose of the study was to assess how closely fermenters can mimic the differences between diets found in vivo. The 4 experimental diets contained forage to concentrate (F:C) ratios of 70:30 (high forage; HF) or 30:70 (high concentrate; HC) with either alfalfa hay (A) or grass hay (G) as the forage. Total bacterial numbers were greater in the rumen of sheep fed HF diets compared with those fed HC diets, whereas the opposite was found in fermenters. The numbers of cellulolytic bacteria were not affected by F:C ratio in any fermentation system, but cellulolytic numbers were 2.7 and 1.8 times greater in sheep than in fermenters for HF and HC diets, respectively. Neither total bacterial nor cellulolytic numbers were affected by the type of forage in sheep or fermenters. Decreasing F:C ratio increased total protozoa and Entodiniae numbers in sheep by about 29 and 25%, respectively, but it had no effect in fermenters. Isotrichidae and Ophryoscolecinae numbers in sheep were not affected by changing F:C ratio, but both disappeared completely from fermenters fed HC diets. Total protozoa and Entodiniae numbers were greater in sheep fed A diets than in those fed G diets, whereas the opposite was found in fermenters. Results indicate that under the conditions of the present study, protozoa population in Rusitec fermenters was not representative of that in the rumen of sheep fed the same diets. In addition, protozoa numbers in fermenters were 121 and 226 times lower than those in the sheep rumen for HF and HC diets, respectively. The automated ribosomal intergenic spacer analysis of the 16S ribosomal DNA was used to analyze the diversity of liquid- and solid-associated bacteria in both systems. A total of 170 peaks were detected in the automated ribosomal intergenic spacer analysis electropherograms of bacterial pellets across the full set of 64 samples, from which 160 were detected in at least 1 individual from each system (sheep or fermenter). Diversity of liquid-associated bacterial pellets was greater with G diets in fermenters but seemed to be unaffected by diet in sheep. Bacterial diversity in solid-associated bacteria pellets was greater for G diets compared with A diets in sheep and fermenters. Different conditions in the fermenters compared with sheep rumen might have caused a selection of some bacterial strains.

Influence of detachment procedure and diet on recovery of solid-associated bacteria from sheep ruminal digesta and representativeness of bacterial isolates as assessed by automated ribosomal intergenic spacer analysis-polymerase chain reaction

Six ruminally and duodenally cannulated sheep were used in a partially replicated 4 × 4 Latin square experiment designed to evaluate the efficiency of 3 detachment procedures (DP) to recover solid-associated bacteria (SAB) from ruminal digesta. The 4 experimental diets contained forage to concentrate (F:C) ratios of 70:30 or 30:70 with either alfalfa hay or grass hay as the forage. Bacterial biomass was labeled with 15NH4Cl. The DP were 1) MET: digesta was incubated at 38°C for 15min with saline solution (0.9% NaCl) containing 0.1% methylcellulose under continuous shaking; 2) STO: digesta was mixed with cold saline solution and homogenized with a stomacher for 5min at 230rpm; 3) FRE: digesta was immediately frozen at −20°C for 72h, thawed at 4°C, mixed with saline solution and subjected to STO procedure. Common to all treatments was storing at 4°C for 24h after the treatment, homogenization, filtration, and resuspension of digesta 2 times in the treatment solutions. The automated ribosomal intergenic spacer analysis of the 16S ribosomal DNA was used to analyze the similarity between bacterial communities attached to the digesta and those in the pellet obtained after each DP. There were no significant F:C × DP or forage × DP interactions for any variable. On average, STO treatment detached 65.8% of SAB from ruminal digesta, about 1.2 and 1.5 times more than FRE and MET treatments, respectively. Total recovery of SAB in STO pellets (48.9%) was greater compared with FRE (31.7%) and MET (33.1%), values being greater for high-forage compared with high-concentrate diets. Similarity index between the bacteria attached to digesta and those in the pellets were lower for FRE (48.2%) compared with MET (54.1%) and STO (54.1%), which suggests that FRE could have destroyed cell integrity of some bacterial species, thus reducing the bacterial diversity present in the pellets. The STO method was the most effective removing SAB from digesta, but only a moderate similarity between the bacterial communities attached to digesta and those recovered in the bacterial pellets was obtained. Values of duodenal microbial flow estimated using SAB as reference bacteria were greater with FRE compared with STO and MET, but all DP detected similar differences between diets, and therefore did not influence the interpretation of results.

In situ ruminal amino acid degradability of green and ensiled Italian rye-grass according to particle transit model and microbial contamination correction

The ruminal degradation of amino acids (AA) of a green Italian rye-grass (GRG) and its silage (ERG) was determined on three wethers cannulated in rumen and duodenum using in situ and particle passage techniques. Wethers were fed a diet of ERG, corn silage and concentrate (1:1:1, DM basis) at 40 g DM/kg BW 0.75. Two rumen incubations (at 0, 2, 4, 8, 16, 24, 48 and 72 h) with freeze-dried samples (3 g) in nylon bags were performed for each feed. The microbial contamination of incubated residues was corrected using 15N enriched solid associated bacteria isolates as reference. Two different estimates of undegraded AA were established: UP p, considering the particle rumen outflow rate ( k p) of the ERG, and UP cp, considering additionally the rate of comminution and mixing ( k c) of these particles. Microbial contamination resulted in large errors in the degradation kinetic parameters of all AA. As a result, non corrected UP p and UP cp included a large fraction of microbial origin. For essential AA plus cysteine these microbial proportions ranged 0.365–0.555 (UP p) and 0.461–0.710 (UP cp) in GRG. In ERG these values ranged: 0.403–0.666 (UP p) and 0.481–0.804 (UP cp). Cysteine always supplied minimum values whereas lysine showed maximum values in GRG or very close to these in ERG. Ensiling was associated with large changes in the AA profile. These variations conditioned, in turn, large differences in the changes made by the rumen microorganisms on the AA profile of both forages. However, ensiling only led to little changes in the profile of the rumen undegraded protein, especially when k c was considered. Results show the need to correct for this contamination to obtain accurate AA valuations and also that the AA profile of the undegraded protein of a green forage may serve as a guide for this profile in its silages.

Role of the protozoan Isotricha prostoma, liquid-, and solid-associated bacteria in rumen biohydrogenation of linoleic acid

From the simultaneous accumulation of hydrogenation intermediates and the disappearance of Isotricha prostoma after algae supplementation, we suggested a role of this ciliate and/or its associated bacteria in rumen biohydrogenation of unsaturated fatty acids. The experiments described here evaluated the role of I. prostoma and/or its associated endogenous and exogenous bacteria in rumen biohydrogenation of C18:2n-6 and its main intermediates CLA c9t11 and C18:1t11. Fractions of I. prostoma and associated bacteria, obtained by sedimentation of rumen fluid sampled from a monofaunated sheep, were used untreated, treated with antibiotics or sonicated to discriminate between the activity of I. prostoma and its associated bacteria, the protozoan or the bacteria, respectively. Incubations were performed in triplicate during 6 h with unesterified C18:2n-6, CLA c9t11 or C18:1t11 (400 μg/ml) and 0.1 g glucose/cellobiose (1/1, w/w). I. prostoma did not hydrogenate C18:2n-6 or its intermediates whereas bacteria associated with I. prostoma converted a limited amount of C18:2n-6 and CLA c9t11 to trans monoenes. C18:1t11 was not hydrogenated by either I. prostoma or its associated bacteria but was isomerized to C18:1c9. A phylogenetic analysis of clones originating from Butyrivibrio-specific PCR product was performed. This indicated that 71% of the clones from the endogenous and exogenous community clustered in close relationship with Lachnospira pectinoschiza. Additionally, the biohydrogenation activity of solid-associated bacteria (SAB) and liquid-associated bacteria (LAB) was examined and compared with the activity of the non-fractioned I. prostoma monofaunated rumen fluid (LAB + SAB). Both SAB and LAB were involved in rumen biohydrogenation of C18:2n-6. SAB fractions performed the full hydrogenation reaction to C18:0 while C18:1 fatty acids, predominantly C18:1t10 and C18:1t11, accumulated in the LAB fractions. SAB and LAB sequence analyses were mainly related to the genera Butyrivibrio and Pseudobutyrivibrio with 12% of the SAB clones closely related to the C18:0 producing B. proteoclasticus branch. In conclusion, this work suggests that I. prostoma and its associated bacteria play no role in C18:2n-6 biohydrogenation, while LAB convert C18:2n-6 to a wide range of C18:1 fatty acids and SAB produce C18:0, the end product of rumen lipid metabolism.

Using microbial fatty acids to improve understanding of the contribution of solid associated bacteria to microbial mass in the rumen

This study sought to distinguish liquid-(LAB) and detached (SAB 1) and undetached (SAB 2) solid-associated bacteria through their fatty acid (FA) and purine base (PB) profiles. Fatty acids and PB were also evaluated as internal microbial markers for estimating microbial biomass associated with rumen particles. Four merino rams fitted with rumen cannulae and fed dehydrated alfalfa pellets provided rumen contents. In 3 consecutive weeks, rumen contents were collected and samples of LAB and SAB 1, total rumen content (TRC), washed rumen particles (WRP) and rumen particles after SAB 1 extraction (ERP) were obtained and analysed for PB and FA. The SAB 2 biomass composition was estimated from the non-NDF organic matter (OM) remaining in ERP. The concentration of total SAB biomass in particles was estimated using both PB and odd and branched-chain fatty acids (OBCFA). Concentrations of PB and OBCFA were highly correlated among the different rumen fractions. Marked differences between LAB and SAB populations occurred with LAB having higher PB content, lower FA content and a higher proportion (g/100 g fatty acids) of OBCFA than did SAB. The chemical composition of SAB 1 and SAB 2 was similar, except for the 15% higher crude protein content of the latter. The concentration of OBCFA (mg/g microbial OM) did not differ between bacterial fractions. The PB/OBCFA ratio (mg/mg) was higher in LAB (2.08) than in SAB (0.94). The ratio between branched-chain and odd-linear-chain FA was higher in LAB (2.26) than in SAB (1.46). Extraction of PB and OBCFA from WRP with our SAB detachment procedure was 61% and 31%, respectively. Estimated SAB 1 and total SAB biomass (mg OM/g WRP) were 158 and 266, and 47 and 164, respectively, using PB and OBCFA as microbial markers. This study suggests that the OBCFA have potential as internal microbial markers in rumen ecosystem studies.