Bacterial community analysis of purulent material from liver abscesses of crossbred cattle and Holstein steers fed finishing diets with or without tylosin

Liver abscesses in feedlot cattle are polymicrobial infections. Culture-based studies have identified Fusobacterium necrophorum as the primary causative agent, but a number of other bacterial species are frequently isolated. The incidence of liver abscesses is highly variable and is affected by a number of factors, including cattle type. Holstein steers raised for beef production have a higher incidence than crossbred feedlot cattle. Tylosin is the commonly used antimicrobial feed additive to reduce the incidence of liver abscesses. The objective of this study was to utilize 16S ribosomal RNA amplicon sequence analyses to analyze the bacterial community composition of purulent material of liver abscesses of crossbred cattle (n = 24) and Holstein steers (n = 24), each fed finishing diet with or without tylosin. DNA was extracted and the V3 and V4 regions of the 16S rRNA gene were amplified, sequenced, and analyzed. The minimum, mean, and maximum sequence reads per sample were 996, 177,070, and 877,770, respectively, across all the liver abscess samples. Sequence analyses identified 5 phyla, 14 families, 98 genera, and 102 amplicon sequence variants (ASV) in the 4 treatment groups. The dominant phyla identified were Fusobacteria (52% of total reads) and Proteobacteria (33%). Of the top 25 genera identified, 17 genera were Gram negative and 8 were Gram positive. The top 3 genera, which accounted for 75% of the total reads, in the order of abundance, were Fusobacterium, Pseudomonas, and Bacteroides. The relative abundance, expressed as percent of total reads, of phyla, family, and genera did not differ (P > 0.05) between the 4 treatment groups. Generic richness and evenness, determined by Shannon–Weiner and Simpson’s diversity indices, respectively, did not differ between the groups. The UniFrac distance matrices data revealed no clustering of the ASV indicating variance between the samples within each treatment group. Co-occurrence network analysis at the genus level indicated a strong association of Fusobacterium with 15 other genera, and not all of them have been previously isolated from liver abscesses. In conclusion, the culture-independent method identified the bacterial composition of liver abscesses as predominantly Gram negative and Fusobacterium as the dominant genus, followed by Pseudomonas. The bacterial community composition did not differ between crossbred and Holstein steers fed finishing diets with or without tylosin.     

Enteric,hepatic and muscle tissue development of goat kids fed with lyophilized bovine colostrum

The objective of this study was to investigate the development of the enteric, hepatic and muscle tissues in goat kids fed with lyophilized bovine colostrum in the transition period of passive immunity to early active immunity. At 0, 7 and 14 h of life, 15 male newborns received 5% of their body weight of lyophilized bovine colostrum and 14 male newborns received goat colostrum, both with 55 mg/ml of IgG. Samples of the duodenum, jejunum, ileum, liver and muscle were collected at 18, 36 and 96 h of life to quantify total protein, DNA and RNA contents. In the jejunum and ileum, the highest levels of total protein and higher protein/RNA ratio were observed at 18 h (p < 0.05). There were no differences in DNA contents in any intestinal segment (p > 0.05). At 96 h, maximum levels of RNA were observed in the jejunum and ileum (p < 0.05) and higher RNA/DNA ratio in the three intestinal segments (p < 0.05), showing increased ability to synthesize intracellular RNA and proteins. The LBC group showed higher protein content and higher protein/DNA and protein/RNA ratios in the jejunum, a higher DNA content in the liver (p < 0.05) and a higher protein/RNA ratio in the muscle tissue (p < 0.05). In the muscle, higher protein and DNA levels were also found at 96 h (p < 0.05). Indicators of cellular activity suggest greater absorption of proteins from lyophilized bovine colostrum and increased cell maturity in the enteric and muscle tissues in the first hours of goat kids' life.     

Characterization of bovine ruminal epithelial bacterial communities using 16S rRNA sequencing, PCR-DGGE, and qRT-PCR analysis

Currently, knowledge regarding the ecology and function of bacteria attached to the epithelial tissue of the rumen wall is limited. In this study, the diversity of the bacterial community attached to the rumen epithelial tissue was compared to the rumen content bacterial community using 16S rRNA gene sequencing, PCR-DGGE, and qRT-PCR analysis. Sequence analysis of 2785 randomly selected clones from six 16S rDNA (～1.4kb) libraries showed that the community structures of three rumen content libraries clustered together and were separated from the rumen tissue libraries. The diversity index of each library revealed that ruminal content bacterial communities (4.12/4.42/4.88) were higher than ruminal tissue communities (2.90/2.73/3.23), based on 97% similarity. The phylum Firmicutes was predominant in the ruminal tissue communities, while the phylum Bacteroidetes was predominant in the ruminal content communities. The phyla Fibrobacteres, Planctomycetes, and Verrucomicrobia were only detected in the ruminal content communities. PCR-DGGE analysis of the bacterial profiles of the rumen content and ruminal epithelial tissue samples from 22 steers further confirmed that there is a distinct bacterial community that inhibits the rumen epithelium. The distinctive epimural bacterial communities suggest that Firmicutes, together with other epithelial-specific species, may have additional functions other than food digestion.     

The Vegetation of the S. A. Lombard Nature Reserve and its Utilisation by Certain Antelope

We examined phylogenetic relationships of the Pachydactylus rugosus complex using DNA sequence data from segments of the mitochondrial genes cytochrome b and 16S ribosomal RNA. These molecular data support the contention that members of the rugosus complex, as defined by McLachlan (1979), form a monophyletic group. Further, high levels of sequence divergence observed between currently recognized subspecies (19.1–26.8 % for cytb), even across short geographic distances, support elevation of each member to full specific rank. The pattern of relationship within the P. rugosus complex species is P. rugosus (P. barnardi, P. formosus). Sequence data provide no evidence to support a close relationship between these taxa and P. capensis, to which previous workers had assigned both P. formosus and P. barnardi.     

Emerging Technologies in Microbial Ecology Aid in Understanding the Effect of Monensin in the Diets of Broilers in Regard to the Complex Disease Necrotic Enteritis

Necrotic enteritis is a complex disease condition of broiler chickens, commercial layer pullets, and turkeys and requires the presence of a toxigenic strain of Clostridium perfringens, alteration of bird diets, and damage to the intestinal epithelium. All of these alone, but especially in combination, result in significant alterations of the intestinal microflora. The intestinal microflora is part of a complex ecosystem that is involved in augmenting intestinal development, immune surveillance, and competitive exclusion against pathogenic organisms. However, when the microflora fails to protect the mucosa from pathogens, antimicrobials are used to reduce the numbers of pathogenic organisms or to prevent their colonization of the intestine. We were interested in studying the effects of monensin on the bacterial community within the ileum of chickens because ionophore antimicrobials are commonly used to prevent Eimeria infections in broilers. We used two 16S ribosomal DNA community analysis protocols, terminal restriction fragment length polymorphism analysis combined with 16S rDNA clone libraries. These methods showed that monensin caused significant alterations in the microbial community structure of the ileum. Whereas the ileal bacterial community of control birds primarily consisted of lactobacilli, monensin-treated birds had communities rich in clostridia. None of the birds exhibited signs of intestinal disease or mucosal lesions, which suggested that the clostridia were avirulent. Although the therapeutic benefits of monensin may largely result from its anticoccidial effects, its ability to foster a competitively exclusive bacterial community may contribute to the intestinal health of birds, thus preventing the development of necrotic enteritis.     

瑞士乳酸杆菌HZ521株的分子鉴定及其部分生物学特性研究

根据GenBank中乳酸杆菌16 S～23 S rRNA基因间沉默区序列设计引物,进一步鏊定猪源乳酸杆菌分离株HZ521;并通过体外试验,以嗜酸乳酸杆菌ATCC 4356为参考菌株,探讨HZ521株的益生素作用.部分16 S～23 S rRNA基因序列同源性分析结果表明,该分离株属于瑞士乳酸杆菌.HZ521株具有较强的产酸能力,能耐受强酸,对Hela细胞的黏附率为87.2%,显著高于ATCC 4356株(P<0.01).表明瑞士乳酸杆菌HZ521株具有益生素特性,可作为肠道益生素的候选菌株.     

Detection of bacterial DNA in synovial fluid from horses with infectious synovitis

Standard culturing techniques are often unrewarding in confirming diagnosis of synovial infection in the equine patient. Several human studies report the use of sensitive polymerase chain reaction (PCR) techniques for the detection of bacterial involvement in acute synovitis. However, successful extraction of bacterial DNA directly from clinical samples from horses without prior culture has not been reported yet. The goal of this study was to develop a sensitive and reliable method for molecular detection and identification of bacterial species in synovial fluid from horses with infectious synovitis. Synovial fluid samples from 6 horses with culture confirmed synovial infection were used for broad range 16S rRNA gene PCR. Synovial aspirates of 2 healthy horses were used as negative controls. Following extraction and purification of synovial fluid DNA, all samples were processed by touchdown PCR. Amplicons were detected by reverse line blot hybridisation and visualised with chemiluminescence. Pathogen-specific detection of 16S rRNA gene sequences was successful in all 6 synovial fluid samples. No bacterial DNA was detected in the aspirates from the negative control horses using touchdown PCR followed by 25 additional cycles of amplification. The identity of the pathogens was confirmed by DNA sequencing of the amplicons. It can be concluded that broad range 16S rRNA gene PCR followed by reverse line blot hybridisation is a promising technique for detection of bacterial DNA in synovial fluid samples. Further research should aim at the detection of bacterial DNA in synovial fluid samples suspected of infection but having negative culture results. When the 16S PCR proves to be reliable and more sensitive than standard culturing techniques, it may become a powerful tool in the diagnosis of synovial infection.     

Estradiol inhibits hepatic stellate cell area and collagen synthesis in the chicken liver

Hepatic stellate cells (HSCs) are the main collagen‐producing cells in the liver. The HSC area and amount of collagen fibers are different between male and female chickens. This study was performed to confirm the effect of estradiol on collagen synthesis in the growing chicken liver. Blood estradiol levels in chicks were compared at 4 and 8 weeks of age, and the collagen fibril network in liver tissue was observed at 8 weeks by scanning electron microscopy. Intraperitoneal administrations of estradiol and tamoxifen to male and female chicks, respectively, were performed daily from 5 to 8 weeks of age. The areas of HSCs and collagen contents were measured in the liver tissue. The blood estradiol level was higher in females than in males, and the collagen fibril network was denser in males than in females at 8 weeks of age. Estradiol administration in males induced decreases in the HSC area and collagen content of the liver. Conversely, tamoxifen administration in females induced an increase in the HSC area but did not facilitate collagen synthesis. Based on these results, estradiol inhibits the area and collagen synthesis of HSCs in the growing chicken liver under normal physiological conditions.     

荷斯坦奶牛瘤胃微生物分离鉴定及多样性分析

研究为分离获得荷斯坦奶牛瘤胃内容物中的细菌,建立系统进化树,获取有益菌种。采用培养组学技术和16S rDNA分子鉴定方法相结合,对3头健康荷斯坦奶牛瘤胃内容物中细菌进行分离培养。共分离得到105株细菌,包括肠球菌属(Enterococcus)共15株14.29%,芽孢杆菌属(bacillus)共11株10.48%,不动杆菌属(Acinetobacter)共14株13.33%,葡萄球菌属(Staphylococcus)共22株20.95%,梭菌属(Clostridium)共1株0.95%,狭义梭菌属(Clostridium sensu stricto)共2株1.90%,短杆菌科(Brevibacteriaceae)共2株1.90%,链球菌属(Streptococcus)共11株10.48%,气球菌属(Aerococcus)共4株3.81%,柠檬酸杆菌属(Citrobacter)共14株13.33%,杆菌属(Brachybacterium)共1株0.95%,克雷伯氏菌属(Klebsiella)共1株0.95%,普罗维登斯菌属(Providencia)共3株2.86%,沙雷氏菌属(Serratia)共4株3.81%。结果中所占比例最高的菌属是葡萄球菌属;系统进化树分析和GenBank中的同源性比对结果发现,从细菌门、纲、目、科、属、种分析,分支明确;26个菌种同源性都在95.01%~100%之间。分离纯化出11株芽孢杆菌属(Bacillus)细菌具有潜在益生菌活性。可作为饲料添加剂饲喂荷斯坦奶牛。     

Diversity and fluctuation in ciliate protozoan population in the rumen of cattle

The purpose of this study was to investigate the diversity and fluctuation in the ciliate protozoan population in the rumen of cattle. DNA was extracted from the rumen of three ruminally cannulated, crossbred cattle and a polymerase chain reaction (PCR)‐derived clone library was constructed, using a specific primer set targeting 18S ribosomal RNA genes of ciliate protozoa. DNA fragments of seven selected clones were validated for standard DNA of the protozoa‐specific real‐time PCR assay. Furthermore, population fluctuation of ciliate protozoa and methanogens in the cattle rumen was determined by real‐time PCR. A total of 60 clones were sequenced, phylogenetically analyzed, and classified into 24 operational taxonomic units (OTUs) based on a 99% similarity criterion. More than 80% sequences were phylogenetically placed in the genus Entodinium. The rest of the sequences were placed in the genus Diploplastron (5%), Dasytricha (8.3%) and Isotricha (3.3%). The results suggest that Entodinium was the dominant group in the rumen of cattle used in this study. The ciliate protozoan population showed no significant change in numbers during the monitoring period and reached a peak at 3 h after feeding. Changes in the protozoa population were lower than those of the methanogens.     

Effect of Fructooligosaccharide on the Structure and Diversity of Rumen Bacterial Community in Dairy Cow by 16S rDNA Sequencing Technology

This experiment was aimed to study the effect of fructooligosaccharides on the structure and diversity of rumen bacterial community in dairy cows by 16S rDNA sequencing technology.Four lactating dairy cows with similar lactation stages and the same parity were randomly divided into two groups using two-phase cross design method.The cows in control group were fed with basal diet and that in test group were fed with the basal diet with 60 g/(d·head) fructooligosaccharides.The experiment was designed through 2×2 cross-over test with 21 d in each stage (14 d for pre-experiment and 7 d for test) and 14 d transitional period of cross test.The rumen fluid samples were collected at 0 (before feeding),2,4,6,9 and 12 h after feeding by cattle catheter.Each phase was collected continuously for 3 days,and the structure and diversity of rumen bacterial community were measured by 16S rDNA sequencing technology.The results of Alpha diversity indexes (Simpson,Shannon),richness indexes (Chao,Ace) and Beta diversity profile showed that the addition of fruitooligosaccharide decreased the bacterial diversity in the rumen of dairy cows.And the results of 16S rDNA sequencing showed that according to the analysis at phylum level,Bacteroidetes,Firmicutes and Proteobacteria accounted for more than 95% of the total bacterial population in cow rumen of two groups.The addition of fructooligosaccharides significantly decreased the abundance of Bacteria_NA (P < 0.05),and the abundance of Synergistetes showed an increasing trend (P=0.075).According to the analysis at genus level,fructooligosaccharides significantly increased the abundance of the Pseudomonas (P < 0.05),extremely significantly increased the abundance of Bacteroides (P < 0.01),while the abundance of Dehalobacterium significantly decreased (P < 0.05).Compared with the control group,the abundance of Ruminococcus,Butyrivibrio,Succiniclasticum and Lachnospiraceae_NA in test group was increased by 80.0%,7.5%,127.9% and 20.0%,respectively,but these differences were not significant (P > 0.05).Under the test conditions,the addition of fructooligosaccharides had a certain effect on the diversity and structure of rumen bacterial flora in dairy cows,which significantly increased the abundance of Pseudomonas which unfermented sugar,extremely significantly increased the abundance of Bacteroides which used carbohydrates as a source of fermentation,had an accelerating effect on the abundance of rumen fiber degrading bacteria.     

Characterization of ileal bacterial microbiota in newly-weaned pigs in response to feeding lincomycin, organic acids or herbal extract

The changes of ileal bacterial microbiota in pigs during the first 2 weeks post-weaning in response to feeding lincomycin, organic acids or herbal extract were characterized using 16S rRNA gene-based PCR-denaturing gradient gel electrophoresis (DGGE) profiling, DNA sequencing, and real-time PCR (QPCR) techniques. Both time post-weaning and the dietary treatments resulted in a shift of the microbiota composition. While time post-weaning mostly influenced Clostridium group, the feed additives increased the population of Lactobacillus and related lactic acid bacteria by ≥ 3-fold.     

Selection and interpretation of clinical pathology indicators of hepatic injury in preclinical studies

This position paper delineates the expert recommendations of the Regulatory Affairs Committee of the American Society for Veterinary Clinical Pathology for the use of preclinical, clinical pathology endpoints in assessment of the potential for drug-induced hepatic injury in animals and humans. Development of these guidelines has been based on current recommendations in the relevant preclinical and human clinical trial literature; they are intended to provide a method for consistent and rigorous interpretation of liver-specific data for the identification of hepatic injury in preclinical studies and potential liability for hepatic injury in human patients.     

The comparison of the collagen fiber contents and hepatic stellate cell distribution in male and female chicken livers

The difference in collagen fiber content, morphological properties and hepatic stellate cell (HSC) distribution was investigated in the liver of both sexes in chicken. Collagen fiber specimens were obtained by maceration treatment with NaOH solution. HSCs were detected using desmin‐specific immunohistochemistry. The ratio of liver weight to body weight was larger in the female than the male chickens. Collagen fiber content, the numerical density of HSCs and the percentage area displaying desmin immunopositivity were not different between the right and left lobes of the liver, in both male and female chickens. However, all of these parameters were larger in the males than the females. In the light microscopic observation, many HSCs in the male had large and elongated cytoplasmic processes. Conversely, HSCs with poorly developed cytoplasmic processes were frequently observed in females. Liver tissue is structurally stronger in male chickens than females and the activity and density of HSCs may be related to the collagen fiber content in chicken liver.     

犬腹腔镜肝部分切除术对肝、肾功能的影响

选择8条健康杂种犬进行腹腔镜下肝部分切除,于麻醉前、术后4h及术后第1、3、5、7、9、11、13、15天采取静脉血进行肝肾功能指标监测.结果显示,天门冬氨酸氨基转移酶、丙氨酸氨基转移酶及碱性磷酸酶于术后第1天升到高峰;尿酸、尿素氮和肌酐于术后4h即达到高峰;白蛋白和总蛋白略微有所下降,于术后第1天降到最低;而r谷氨酰基转移酶术后变化不大.结果表明,犬腹腔镜肝部分切除术仅仅短期内对肝、肾功能产生影响,且肝、肾功能在术后一段时间内可恢复.     

冬夏季长白猪精液中细菌多样性与精子质量特性关联分析

为探究冬夏季长白猪精液中细菌多样性变化和精子质量特性之间的相关性,利用16S rRNA基因高通量测序技术得到冬夏季长白猪精液中微生物的特征序列(ASV),计算机辅助精子分析系统(CASA)分析冬夏季精子活力参数指标的变化.结果 显示:长白猪精液中细菌多样性在冬夏季之间差异显著(P＜0.05),门水平冬季优势菌群为厚壁菌...     

黄花棘豆在腐解过程中的化感作用及其土壤细菌群落结构分析

黄花棘豆属豆科棘豆属多年生草本植物,是我国西部草场广泛分布的主要毒草之一,为了探索黄花棘豆的危害机制,揭示其发生发展规律,本研究通过模拟黄花棘豆在土壤中的腐解过程,检测其对紫花苜蓿和黑麦草两种牧草的化感作用。结果显示当土壤中含有质量分数为5%的黄花棘豆时,黄花棘豆在腐解过程中就会对两种牧草的生长产生显著的化感抑制作用,其中对紫花苜蓿的化感作用更为明显。同时通过细菌16S rDNA测序对黄花棘豆根系土和非根系土中的细菌群落进行了比较,结果显示土壤细菌群落中的部分分类单元,如变形菌门(Proteobacteria)、放线菌门(Actinobacteria)和酸杆菌门(Acidobacteria)的比例在两组中存在显著差异;同时,非根系土的细菌群落多样性高于根系土。以上结果相结合表明黄花棘豆可能通过化感作用改变其生长土壤的微生物环境,在促进自身生长的同时降低不良微生物对其自身的影响,并抑制其他共生植物生长。本研究为更好地寻找黄花棘豆的有效防控提供了一定理论依据。     

A combination of Lactobacillus buchneri and Pediococcus pentosaceus extended the aerobic stability of conventional and brown midrib mutants–corn hybrids ensiled at low dry matter concentrations by causing a major shift in their bacterial and fungal community

We evaluated the effects of applying a combination inoculant to four corn hybrids harvested at high moisture on their nutritive value and microbial populations. The treatment design was the factorial combination of corn hybrids ensiled with (INO) and without (CON) inoculant. The hybrids were TMF2R737 (MCN), F2F817 (MBR), P2089YHR (PCN), and PI144XR (PBR), ensiled at dry matter (DM) concentrations of 30.5%, 26.3%, 31.1%, and 31.5%, respectively; MBR and PBR were brown midrib mutants (BMR). The inoculant contained Lactobacillus buchneri and Pediococcus pentosaceus (4 × 10⁵ and 1 × 10⁵ cfu/g of fresh corn). The experiment had a complete randomized design with treatments replicated six times. Corn was treated or not with inoculant, packed into 7.6 L bucket silos, and stored for 100 d. At d 0, the relative abundance (RA, %) of Enterobacteriaceae was lower in PBR vs. the other hybrids [51.3 vs. x¯ = (average of) 58.4] and in the case of fungi, incertae sedis (i.s.) Tremellales and Mucoraceae were more and less abundant, respectively, in conventional hybrids vs. BMRs (x¯= 25.8 vs. x¯ = 13.9 and x¯ = 3.64 vs. x¯ = 7.52; P < 0.04). After ensiling, INO had higher LAB (9.3 vs. 7.1 log cfu/g of fresh corn) and acetic acid (3.44% vs. 1.32% of DM) and lower yeast (3.1 vs. 4.6) and molds (1.5 vs. 3.0), and also extended the aerobic stability (582 vs. 111 h) but decreased DM recovery (95.6% vs. 97.4%) vs. CON (P < 0.02). Inoculation reduced bacterial phylogenetic diversity (6.75 vs. 14.4) but increased fungal observed taxonomical units (46 vs. 20) vs. CON (P < 0.01). Also, a higher relative abundance (RA) for Lactobacillaceae (99.2% vs. 75.7%) and lower for Enterobacteriaceae (0.28 vs. 9.93) was observed due to inoculation (P < 0.001). For fungi, INO had a lower RA compared to CON for Monascaceae (12.6 vs. 44.7) and increased i.s. Tremellales (8.0 vs. 1.2) and i.s. Saccharomycetales (6.4% vs. 0.3%; P < 0.006). Inoculation changed the diverse bacterial community found in the phyllosphere across hybrids to a taxonomically uneven one dominated by Lactobacillaceae. In the case of fungi, INO application increased the fungal diversity at d 100 mainly by reducing the dominance of Monascaceae vs. CON. In conclusion, the INO treatment overwhelmed the disparate microbial populations found across BMR and conventional hybrids ensiled at low DM concentrations and ensured a significant concentration of acetic acid that modified fungal populations and in turn extended the aerobic stability of all hybrids.