The deferred growth inhibition assay can be used to assess the competition effect by one bacterial isolate on another. Inhibition is quantified by measuring the zone of clearing around the inhibitor-producing isolate, or qualitatively assessed by determining the visible extent of inhibition.
Competitive exclusion can occur in microbial communities when, for example, an inhibitor-producing strain outcompetes its competitor for an essential nutrient or produces antimicrobial compounds that its competitor is not resistant to. Here we describe a deferred growth inhibition assay, a method for assessing the ability of one bacterium to inhibit the growth of another through the production of antimicrobial compounds or through competition for nutrients. This technique has been used to investigate the correlation of nasal isolates with the exclusion of particular species from a community. This technique can also be used to screen for lantibiotic producers or potentially novel antimicrobials. The assay is performed by first culturing the test inhibitor-producing strain overnight on an agar plate, then spraying over the test competitor strain and incubating again. After incubation, the extent of inhibition can be measured quantitatively, through the size of the zone of clearing around the inhibitor-producing strain, and qualitatively, by assessing the clarity of the inhibition zone. Here we present the protocol for the deferred inhibition assay, describe ways to minimize variation between experiments, and define a clarity scale that can be used to qualitatively assess the degree of inhibition.
Bacteria living in communities compete at the interspecific and intraspecific level for space and nutrients 6. Competition between microbes can often lead to exclusion of particular species or strains within a community. Exclusion can be due to competition for a particular receptor or nutrient, or the production of an antimicrobial compound by a member of the community 6.
Studies investigating competitive exclusion frequently examine the presence and absence of species using 16S rRNA sequencing 3,4,13. However, intraspecific trait variation, for example the presence or absence of antimicrobial peptide production, can hugely impact the ability of one species to inhibit another 1. Since 16S rRNA sequencing cannot distinguish between strains of the same species, intraspecific trait variation cannot be assessed. The technique described here can be used to assess the potential of individual strains to exclude other bacteria. This method has previously been used to show a positive correlation between the presence of Staphylococcus aureus inhibitory bacteria and the absence of S. aureus in a nasal community 7.
The deferred growth inhibition (competition) assay can identify production of antimicrobial compounds or nutrient competition by the inhibitor strain. It can also detect positive interactions, whereby the presence of the inhibitor strain actually improves the growth of the competitor strain. This assay can be used to create quantitative data (zone of clearing size) and qualitative data (degree of inhibition), both of which can be overlaid onto data of the presence or absence of a species within a community to find correlations between phenotype (trait) and competitive exclusion 7.
从其他人的区别就这个细菌物种竞争协议的一个关键步骤,是抑制剂的孵育过夜除了竞争对手分离的前隔离开来。抑制剂应变需要这种增长时期产生的抑制化合物。作为竞争者菌株在相同介质的顶部重叠,此方法允许研究人员观察到的全部潜力 抑制剂菌株,干扰竞争者菌株的生长。其结果是,该测定反映了与自然发生的情况;一个孤立完全建立在一个利基,另一个必须能够抵消任何抑制变量能够成功入侵的利基。
有两个部分,以该协议最有可能执行的,如果不正确会导致错误的结果。首先,蒸发器瓶杀菌不完全可以引进污染细菌进入检测。 INCU用于冲洗汽化器瓶在步骤3.6在无菌容器中的肉汤bation可以用来确认瓶完全灭菌。在消毒液,如卫可附加洗涤,可先于表面活性清洁剂洗涤,在步骤3.2中所述,如果需要额外的杀菌使用。
可能导致错误的结果的第二步骤是竞争者菌株(步骤6.1)的稀释液。如果稀释并非最佳,抑制的明确测量可能不容易确定。该测定是使用不同的鼻菌株作为抑制剂生产在大范围的革兰氏阳性和革兰氏阴性物种与链球菌菌株优化金黄色葡萄球菌 SH1000作为竞争对手的应变7,8。它后来被用各种凝固酶阴性和凝固酶阳性葡萄球菌作为竞争对手和抑制剂生产菌株进行测试。当测试除上述作为竞争者其他属应变,对于接种稀释的一些优化可能是必要的。
如果清晰度分数重复之间显著变化,可能有必要通过将其设置为特定的光学密度进行标准化竞争者菌株接种物。然而,这将增加该测定需要来设置,并有可能降低菌株的量是可能每个实验进行处理的时间。在视觉上调整文化,用麦氏标准可以提供快速的替代适当的OD。
这种技术的一个限制是,它只能适用于培养细菌。这就是为什么许多研究使用的16S rRNA测序预测竞争排斥相互作用3,4,13。然而,遗传和宏基因组技术只能社区成员区分的物种水平,和/或不考虑特定种内性状的变化。能够筛选一个particul的关联AR基因,该基因编码具有细菌物种5的存在或不存在的性状,但是这需要可能与一个物种的排斥相关联的基因的预先知识。
这种技术的安全性的考虑是,由于气雾产生的细菌,它只能在实验室使用具有2级安全柜,或具有类似的安全预防措施。有替代技术测试为占种内性状变异,不产生细菌菌株气溶胶之间的竞争。一种这样的方法是同时拮抗试验2。在该方法中,一个分离株的接种物涂布在琼脂平板和第二分离接种物点样或刺伤顶部一旦第一已干燥。这将产生其中菌株直接竞争(同时对抗)的环境中,既竞争产生的抑制化合物和第一清除营养素。该advantag递延生长抑制试验在同时对抗法的e是该抑制剂分离应该总是有竞争对手分离的入侵之前被完全建立竞争优势。这是更加反射性的环境中,会发生什么,因为在大多数龛,加入前另一个应变,而不是在同一时间8被加入了两个分离一种隔离群将被建立。
另一种替代,以避免气溶胶的产生菌的是添加竞争者隔离在顶层琼脂,这可能是倾而不是喷洒在抑制剂分离物。然而,上层琼脂中加入的体积将需要约3毫升至确保即使板的覆盖范围。在该卷中,竞争者分离物将不为相同的介质作为抑制剂分离物上生长,所以将不从减少营养物受损。竞争对手也不会与任何UNT抑制化合物直接接触IL它们扩散到顶层琼脂。这样一个试验不能被描述为递延抑制或同时拮抗作用。
类似的方法以前已经用来评估之间临床S.杆菌肽抗性水平金黄色葡萄球菌菌株10。由10描述这里描述的协议和之间的主要区别,是后者只分类竞争者菌株为敏感(完成inhibition-清晰度评分0)或抗性(部分无inhibition-清晰度分数1-5)。延迟生长抑制试验可以因此还可以用于筛选对特定抗微生物剂,或者甚至是生产者的抗性水平来搜索对耐多药病原体活性新颖抗微生物剂。
有人建议,该宿主微生物可以被操纵以消除细菌群落9的不希望的成员。棒状杆菌或金黄色葡萄球菌中的应用ylococcus表皮已经被证明消除S.葡萄球菌定植在人口11,12的一个显著比例鼻孔。因此,研究为特定菌株能竞争排除主机菌群的不良成员,通过技术如这里所描述的人,可能会导致未来的治疗。
The authors have nothing to disclose.
JCM由BBSRC-IPA奖与联合利华公司(BB / L023040 / 1)资助。 HAG由高等教育博士助学金的沙特阿拉伯教育部资助。
Brain heart infusion broth | Lab M | lab049 | rich general purpose media |
agar-agar | Merck Milipore | 101614 | |
petri dishes | Sarstedt | 82.1473.001 | |
plastic perfume vaporizer | not known | – | 10 cm high with 3.5 cm diameter clear plastic spray bottle with lid, purchased from the travel section of a supermarket |
Universal bottles | no longer in production, alternative SLS BOT5006 | 28 ml glass cylindrical bottle (approx 280 mm diameter, 850 mm height), flat bottomed with plastic screw cap | |
Decon 90 | Decon | surface active cleaning agent |