Veterinary ocular microbiome: Lessons learned beyond the culture

Ocular pathogens cause many painful and vision‐threatening diseases such as infectious keratitis, uveitis, and endophthalmitis. While virulent pathogens and pathobionts play important roles in disease pathogenesis, the scientific community has long assumed disruption of the ocular surface occurs prior to microbial colonization and subsequent infection. While nonpathogenic bacteria are often detected in corneal and conjunctival cultures from healthy eyes, cultures also frequently fail to yield growth of common ocular pathogens or nonpathogenic bacteria. This prompts the following question: Is the ocular surface populated by a stable microbial population that cannot be detected using standard culture techniques? The study of the microbiome has recently become a widespread focus in physician and veterinary medicine. Research suggests a pivotal symbiotic relationship with these microbes to maintain healthy host tissues, and when altered is associated with various disease states (“dysbiosis”). The microbiota that lives within and on mammalian bodies have long been known to influence health and susceptibility to infection. However, limitations of traditional culture methods have resulted in an incomplete understanding of what many now call the “forgotten organ,” that is, the microbiome. With the introduction of high‐throughput sequencing, physician ophthalmology has recognized an ocular surface with much more diverse microbial communities than suspected based on traditional culture. This article reviews the salient features of the ocular surface microbiome and highlights important future applications following the advent of molecular techniques for microbial identification, including characterizing ocular surface microbiomes in our veterinary species and their potential role in management of infectious and inflammatory ocular diseases.     

Current ocular microbiome investigations limit reproducibility and reliability: Critical review and opportunities

Enthusiasm for research describing microbial communities using next‐generation sequencing (NGS) has outpaced efforts to standardize methodology. Without consistency in the way research is carried out in this field, the comparison of data between studies is near impossible and the utility of results remains limited. This holds true for bacterial microbiome research of the ocular surface, and other sites, in both humans and animals. In addition, the ocular surface remains under‐explored when compared to other mucosal sites. Low bacterial biomass samples from the ocular surface lead to further technical challenges. Taken together, two major problems were identified: (1) Normalization of the workflow in studies utilizing NGS to investigate the ocular surface bacteriome is necessary in order to propel the field forward and improve research impact through cross‐study comparisons. (2) Current microbiome profiling technology was developed for high bacterial biomass samples (such as feces or soil), posing a challenge for analyses of samples with low bacterial load such as the ocular surface. This article reviews the challenges and limitations currently facing ocular microbiome research and provides recommendations for minimum reporting standards for veterinary ophthalmologists and clinician scientists to limit inter‐study variation, improve reproducibility, and ultimately render results from these studies more impactful. The move toward normalization of methodology will expedite and maximize the potential for microbiome research to translate into meaningful discovery and tangible clinical applications.     

The impact of rumen cannulation on the microbial community of goat rumens as measured using 16S rRNA high‐throughput sequencing

The main objective of this study was to determine the impact of rumen cannulation on the microbial community of goat rumens using 16S rRNA high‐throughput sequencing. Twelve Boer crossbred goats were used in the experiment: six goats were surgically fitted with rumen cannula, and the other six were used as controls. All goats were fed the same diet for 20 days, after which their rumen digesta were sampled once per week for three consecutive weeks. Total microbial DNA was extracted from the collected rumen fluid and was used as a template to amplify the V4 hypervariable region of the 16S rRNA gene. High‐throughput sequencing was performed using an Illumina MiSeq platform, and the sequences were analyzed primarily using the Quantitative Insights into Microbial Ecology pipeline software. The results showed that the Chao 1 index, the observed species index and the Shannon‐Wiener index were not significantly different (p > 0.05) between the two groups. Bacteroidetes, Firmicutes, Tenericutes were the predominant phylum in both groups, and their relative abundance was 60.63%, 29.48%, 2.24% (n = 6, CT group) and 61.17%, 26.92%, 1.66% (n = 6, RC group) respectively. At the phylum level, the relative abundance of Proteobacteria was significantly higher (p < 0.001) in the microbial communities of RC goats, and Planctomycetes and Chloroflexi were significantly lower (p = 0.02). The abundances of other phyla were not significantly different between treatments. A total of 19 lower‐level taxa also exhibited significant differences (p < 0.05) in relative abundance between the groups. In addition, there were 18 genera shared within the control group, 26 shared within the rumen‐cannulated group, and 16 shared by both groups. Prevotella was the most abundant shared genus, although its abundance was not significantly different (p > 0.05) between the groups. In conclusion, although the most abundant microbes kept stable, rumen cannulation had the potential to significantly change rumen microbial communities in goats.     

不同饲粮条件下湖北黑头羊瘤胃细菌多样性及群落结构分析

旨在研究不同饲粮条件下湖北黑头羊瘤胃细菌多样性及群落结构。选取15只健康的湖北黑头山羊公羊,随机分为5组,每组3只,分别饲喂花生藤(A组)、苜蓿(B组)、苜蓿+花生藤(C组)为粗饲料来源的颗粒型全混合日粮以及进口苜蓿草颗粒(D组)和新疆苜蓿草颗粒(E组),试验期共45 d,其中预试期15 d。在试验结束后第1天,经口腔抽取瘤胃液抽提基因组DNA,采用Illumina Miseq PE300平台对瘤胃细菌进行分析。结果表明:1)在97%相似性水平下,5组样品共产生851个操作分类单元(OTU),共享295个OTU,占瘤胃液细菌总OTU数目的34.67%,D组在各组中α多样性指数指标(Ace指数、Chao1指数和Shannnon指数)最高,而3组颗粒型全混合日粮中A、C组高于B组(P<0.05,P<0.01);2)瘤胃中拟杆菌门(Bacteroidetes)、厚壁菌门(Firmicutes)、无壁菌门(Tenericutes)为各组优势菌门,D组中的拟杆菌门显著高于B组(P<0.05),而厚壁菌门显著低于D组(P<0.05),而A、B、C组间拟杆菌门、厚壁菌门含量差异不显著(P>0.05);3)普雷沃氏菌属1(Prevotella_1)、1种未鉴定的属(Unidentified genus)、理研菌属RC9(Rikenellaceae_RC9_gut_group)为优势菌属,其中D组普雷沃氏菌属含量较高,A组与C组,D组与E组的遗传距离更接近。综合得出,苜蓿草颗粒品质和颗粒型全混合日粮中精料含量能影响湖北黑头羊瘤胃细菌的多样性;全苜蓿饲粮条件下湖北黑头羊瘤胃存在独特的细菌群落结构,细菌多样性最高。     

Ruminal microbiota composition associated with ruminal fermentation parameters and milk yield in lactating buffalo in Guangxi,China—A preliminary study

The ruminal microbiota of 15 dairy buffalo was characterized using high‐throughput 16S rRNA gene amplicon sequencing. Results showed that Bacteroidetes was the dominant bacterial phylum in all rumen samples, followed by Firmicutes, Proteobacteria, Tenericutes and Verrucomicrobia. Butyrivibrio was positively correlated with average milk fat yield (R = 0.55; p = 0.03), average milk total solid yield (R = 0.56; p = 0.03) and standard milk yield (R = 0.52; p = 0.05). Acinetobacter were positively correlated with average milk protein yield (R = 0.56; p = 0.03), average milk total solid yield (R = 0.60; p = 0.02) and standard milk yield (R = 0.57; p = 0.03). Acetobacter was positively correlated with acetate (R = 0.63; p = 0.01), propionate content (R = 0.55; p = 0.03), butyrate content (R = 0.61; p = 0.02) and total VFA (R = 0.62; p = 0.01). The phyla Proteobacteria (R = 0.53; p = 0.04) and genus Prevotella (R = 0.52; p = 0.05) were positively correlated with butyrate content. Correlation analysis suggested that increased Butyrivibrio and Acinetobacter residing in the buffalo rumen could improve milk performance.     

Canine ocular onchocerciasis in the United States: two new cases and a review of the literature

Since 1991, 53 cases of canine ocular onchocerciasis have been reported in the literature worldwide, 43 of these were from Greece, five from Hungary, and five from the western United States. Information on the histopathologic features of canine ocular onchocerciasis is limited. We describe the histopathologic features of canine ocular onchocerciasis in two dogs from California that presented clinically with firm episcleral nodules and uveitis unilaterally. Pertinent literature and pathogenesis are reviewed; recognizable clinical features and treatment are discussed. The cases presented were diagnosed via histopathology of the enucleated globes and episcleral granulomas at the Comparative Ocular Pathology Laboratory of Wisconsin (COPLOW). Positive identification of adult Onchocerca within episcleral granulomas was made based on light-microscopy features. Histopathologic examination of both globes revealed episcleral parasites surrounded by granulomas containing few to moderate numbers of eosinophils. Other sequelae, in both cases, included lymphoplasmacytic uveitis, preiridal fibrovascular membranes, peripheral anterior synechiae, retinal degeneration, and optic nerve head cupping. Both male and female worms were present, as were in utero microfilariae in both cases. Worms in both cases were tentatively identified as Onchocerca lienalis. Ocular onchocerciasis should be a differential consideration in cases of canine conjunctival nodules or periorbital swelling, particularly in dogs from the western United States.     

不同种植年限条件下黄花蒿根际土壤微生物生物量、酶活性及真菌群落组成

试验采集未种植、种植1年、3年和5年的黄花蒿根际土壤,采用常规分析和Illumina MiSeq高通量测序技术,研究了土壤微生物生物量、酶活性及真菌群落组成。结果表明,在人工种植黄花蒿的土壤中,微生物生物量碳氮减少,碳氮比例改变;脱氢酶、脲酶和蔗糖酶活性降低,酸性磷酸酶活性增强;说明黄花蒿释放的化感物质选择性抑制了土壤微生物生长、繁殖和代谢。在不同种植年限的土壤中,主成分分析显示代表不同种植年限土壤真菌群落的点在坐标图中分布距离较远,表明它们的群落组成发生了显著变化(P<0.05)。此外,子囊菌门占土壤真菌的66.10%~95.28%,黄花蒿种植时间影响真菌门类和优势真菌的丰富度。在前20种优势真菌中,有14种共存于不同种植年限的土壤中,每种土壤中存在1~3种独有真菌,说明土壤是决定真菌种群组成的主导因素,又因种植黄花蒿而改变。在栽培1~5年的黄花蒿土壤中,优势菌株中出现蒿属的常见病菌——蒿白粉菌和艾菊柄锈菌,提高相应病害的发生风险。     

Dietary protein levels and amino acid supplementation patterns alter the composition and functions of colonic microbiota in pigs

Different dietary nitrogen (N) patterns may have different effects on gut microbiota. To investigate the effects of different crude protein (CP) levels or essential amino acids (EAA) supplementation patterns on the structure and functions of colonic microbiota, 42 barrows (25 ± 0.39 kg) were randomly assigned to 7 dietary treatments including: diet 1, a high CP diet with balanced 10 EAA; diet 2, a medium CP diet with approximately 2% decreased CP level from diet 1 and balanced 10 EAA; diets 3, 4, 5, 6 and 7, low CP diets with 4% decreased CP level from diet 1. Specifically, diet 3 was only balanced for Lys, Met, Thr and Trp; diets 4, 5 and 6 were further supplemented with Ile, Val and Ile + Val on the basis of diet 3, respectively; and diet 7 was balanced for 10 EAA. Results over a 110-d trial showed that reducing the CP level by 2% or 4% dramatically decreased N intake and excretion (P < 0.05) in the presence of balanced 10 EAA, which was not observed when altering the EAA supplementation patterns in low CP diet (−4%). With balanced 10 EAA, 2% reduction in dietary CP significantly reduced Firmicutes-to-Bacteroidetes (F:B) ratio and significantly elevated the abundance of Prevotellaceae NK3B31 (P < 0.05); whereas 4% reduction evidently increased the abundances of Proteobacteria, Succinivibrio and Lachnospiraceae XPB1014 (P < 0.05). Among the 5 low CP diets (−4%), supplementation with Ile, or Val + Ile, or balanced 10 EAA increased F:B ratio and the abundance of Proteobacteria. In addition, the predicted functions revealed that different CP levels and EAA balanced patterns dramatically altered the mRNA expression profiles of N-metabolizing genes, the “N and energy metabolism” pathways or the metabolism of some small substances, such as amino acids (AA) and vitamins. Our findings suggested that reducing the dietary CP levels by 2% to 4% with balancing 10 EAA, or only further supplementation with Ile or Val + Ile to a low protein diet (−4%) reduced the N contents entering the hindgut to various degrees, altered the abundances of N-metabolizing bacteria, and improved the abilities of N utilization.     

Nerve growth factor in dogs: Assessment of two immunoassays and selected ocular parameters following a nicergoline challenge per os

Impairment of corneal nerves can result in the development of ocular surface diseases such as aqueous tear deficiency and neurotrophic keratopathy. This study investigates oral nicergoline, an α‐adrenoceptor antagonist shown to enhance endogenous secretion of nerve growth factor (NGF) by the lacrimal gland, as a potential therapy for these conditions. Five female spayed Beagle dogs received a 2‐week course of oral nicergoline (10 mg twice daily). Drug safety was evaluated with ophthalmic and physical examinations, blood pressure monitoring, bloodwork, and urinalysis. The effect of nicergoline on the ocular surface was assessed with corneal esthesiometry, Schirmer tear test‐1, and tear film breakup time. Drug effect on NGF levels was assessed by collecting tears and blood at baseline and completion of therapy using a bead‐based immunoassay and an enzyme‐linked immunosorbent assay. Although nicergoline was well tolerated in all dogs, it did not have a significant impact on corneal sensitivity, tear production, or tear stability. Of note, NGF was below the limit of quantification in all tear samples and was only detected in 8/20 serum samples with no significant difference between levels at baseline (189.4 ± 145.1 pg/mL) and completion of therapy (149.4 ± 79.4 pg/mL). Further validation of NGF analytical assays is warranted before nicergoline is investigated in clinical patients.     

基于高通量测序的准噶尔盆地荒漠土壤细菌多样性及群落结构特征

荒漠草地占新疆草地总面积的46.9%,不同荒漠类型的气候差异显著,植被和土壤类型也各不相同。以准噶尔盆地大面积分布的3种代表性荒漠植被类型(南缘伊犁绢蒿荒漠、腹地白梭梭荒漠和北缘盐生假木贼荒漠)为研究对象,应用高通量测序技术,分析比较3种荒漠植被类型的土壤细菌群落组成和多样性特征。结果表明:放线菌门、变形菌门、绿弯菌门、酸杆菌门、芽单胞菌门和拟杆菌门是准噶尔盆地荒漠土壤中6个主要优势类群细菌,其相对丰度累计超过94%。放线菌门在3种荒漠类型中相对丰度最高,均超过50%,但差异不显著(P>0.05);酸杆菌门在伊犁绢蒿荒漠中相对丰度最高,厚壁菌门在白梭梭荒漠丰度最高,拟杆菌门在盐生假木贼荒漠丰度最高,且这3种菌门在3种荒漠类型中差异显著(P<0.05);在3种荒漠类型中,白梭梭荒漠细菌操作分类单元(OTU)数最少,多样性最低。Pearson相关性分析和RDA分析结果均表明,年均降水量和土壤有机碳是影响细菌群落结构组成和多样性最显著的环境因子。     

Evaluation of a novel animal milk oligosaccharide biosimilar: macronutrient digestibility and gastrointestinal tolerance,fecal metabolites,and fecal microbiota of healthy adult dogs and in vitro genotoxicity assays

Milk oligosaccharides (MO) are bioactive compounds in mammalian milk that provide health benefits to neonates beyond essential nutrients. GNU100, a novel animal MO biosimilar, was recently tested in vitro, with results showing beneficial shifts in microbiota and increased short-chain fatty acid (SCFA) production, but other effects of GNU100 were unknown. Three studies were conducted to evaluate the safety, palatability, and gastrointestinal (GI) tolerance of GNU100. In study 1, the mutagenic potential of GNU100 was tested using a bacterial reverse mutation assay and a mammalian cell micronucleus test. In study 2, palatability was assessed by comparing diets containing 0% vs. 1% GNU100 in 20 adult dogs. In study 3, 32 adult dogs were used in a completely randomized design to assess the safety and GI tolerance of GNU100 and explore utility. Following a 2-wk baseline, dogs were assigned to one of four treatments and fed for 26 wk: 0%, 0.5%, 1%, and 1.5% GNU100. On weeks 2, 4, and 26, fresh fecal samples were collected to measure stool quality, immunoglobulin A, and calprotectin, and blood samples were collected to measure serum chemistry, inflammatory markers, and hematology. On weeks 2 and 4, fresh fecal samples were collected to measure metabolites and microbiota. On week 4, total feces were collected to assess apparent total tract macronutrient digestibility. Although revertant numbers were greater compared with the solvent control in tester strain WP2uvrA(pKM101) in the presence of metabolic activation (S9) in the initial experiment, they remained below the threshold for a positive mutagenic response in follow-up confirmatory tests, supporting that GNU100 is not mutagenic. Similarly, no cytotoxicity or chromosome damage was observed in the cell micronucleus test. The palatability test showed that 1% GNU100 was strongly preferred (P < 0.05; 3.6:1 consumption ratio) over the control. In study 3, all dogs were healthy and had no signs of GI intolerance or illness. All diets were well accepted, and food intake, fecal characteristics, metabolite concentrations, and macronutrient digestibilities were not altered. GNU100 modulated fecal microbiota, increasing evenness and Catenibacterium, Megamonas, and Prevotella (SCFA producers) and reducing Collinsella. Overall, the results suggest that GNU100 is palatable and well-tolerated, causes no genotoxicity or adverse effects on health, and beneficially shifts the fecal microbiota, supporting the safety of GNU100 for the inclusion in canine diets.     

VEGFR‐2 expression in malignant tumours of the canine mammary gland: a prospective survival study

Vascular endothelial growth factor receptor‐2 (VEGFR‐2) is the main receptor activated by vascular endothelial growth factor ‐A (VEGF‐A) to promote tumour angiogenesis. Its clinical prognostic value has not been studied in canine mammary tumours (CMTs). Dogs with mammary cancer were enrolled in a survival study and the immunohistochemical expressions of VEGFR‐2 and VEGF‐A were analysed and associated with clinicopathological features. VEGFR‐2 expression was associated with VEGF immunoreactivity in cancer cells, supporting the presence of an autocrine loop that may be involved in CMTs growth and survival. VEGFR‐2 was also expressed by endothelial cells from tumour vasculature and positively associated with stromal matrix metalloproteinase‐9 (MMP‐9), suggesting the existence of a link between endothelial cells activation and up‐regulation of matrix degrading proteins. Carcinosarcomas exhibited high VEGFR‐2 expression suggesting that it may be one of the activated molecular pathways in this aggressive histological type and that VEGFR‐2 inhibitors may constitute a potential treatment to improve the prognosis of these patients. Both VEGF and VEGFR‐2 immunoreactivities were independent of patients' overall survival (OS) and disease‐free survival (DFS).