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Abstract：
Haemophilus and Aggregatibacter are two of the most common bacterial genera in the human oral cavity, encompassing both commensals and pathogens of substantial ecological and medical significance. In this study, we conducted a metapangenomic analysis of oral Haemophilus and Aggregatibacter species to uncover genomic diversity, phylogenetic relationships, and habitat specialization within the human oral cavity. Using three metrics-pangenomic gene content, phylogenomics, and average nucleotide identity (ANI)-we first identified distinct species and sub-species groups among these genera. Mapping of metagenomic reads then revealed clear patterns of habitat specialization, such as Aggregatibacter species predominantly in dental plaque, a distinctive Haemophilus parainfluenzae sub-species group on the tongue dorsum, and H. sp. HMT-036 predominantly in keratinized gingiva and buccal mucosa. In addition, we found that supragingival plaque samples contained predominantly only one out of the three taxa, H. parainfluenzae, Aggregatibacter aphrophilus, and A. sp. HMT-458, suggesting independent niches or a competitive relationship. Functional analyses revealed the presence of key metabolic genes, such as oxaloacetate decarboxylase, correlated with habitat specialization, suggesting metabolic versatility as a driving force. Additionally, heme synthesis distinguishes H. sp. HMT-036 from closely related Haemophilus haemolyticus, suggesting that the availability of micronutrients, particularly iron, was important in the evolutionary ecology of these species. Overall, our study exemplifies the power of metapangenomics to identify factors that may affect ecological interactions within microbial communities, including genomic diversity, habitat specialization, and metabolic versatility.
OBJECTIVE: Understanding the microbial ecology of the mouth is essential for comprehending human physiology. This study employs metapangenomics to reveal that various Haemophilus and Aggregatibacter species exhibit distinct ecological preferences within the oral cavity of healthy individuals, thereby supporting the site-specialist hypothesis. Additionally, it was observed that the gene pool of different Haemophilus species correlates with their ecological niches. These findings shed light on the significance of key metabolic functions in shaping microbial distribution patterns and interspecies interactions in the oral ecosystem.
OBJECTIVE: Understanding the microbial ecology of the mouth is essential for comprehending human physiology. This study employs metapangenomics to reveal that various Haemophilus and Aggregatibacter species exhibit distinct ecological preferences within the oral cavity of healthy individuals, thereby supporting the site-specialist hypothesis. Additionally, it was observed that the gene pool of different Haemophilus species correlates with their ecological niches. These findings shed light on the significance of key metabolic functions in shaping microbial distribution patterns and interspecies interactions in the oral ecosystem.
摘要：
嗜血杆菌和Aggregatibacter是人类口腔中最常见的两个细菌属，包括共生体和具有重大生态和医学意义的病原体。在这项研究中,我们对口服嗜血杆菌和Aggregatibacter物种进行了基因组分析，以揭示基因组多样性，系统发育关系，和人类口腔内的栖息地专业化。使用三个指标-全基因组基因含量，系统基因组学，和平均核苷酸同一性（ANI）-我们首先在这些属中确定了不同的物种和亚种组。宏基因组读数的映射然后揭示了清晰的栖息地专业化模式，例如主要存在于牙菌斑中的Aggregatibacter物种，舌背上一个独特的副流感嗜血杆菌亚种组，和H.sp.HMT-036主要存在于角化牙龈和颊粘膜中。此外,我们发现牙龈上菌斑样本主要只包含三个分类单元中的一个，H.副流感，失星症聚集杆菌,和A.sp.HMT-458，建议独立的利基市场或竞争关系。功能分析揭示了关键代谢基因的存在，如草酰乙酸脱羧酶，与栖息地专业化相关，表明代谢多功能性是一种驱动力。此外,血红素合成区分H.sp.HMT-036来自密切相关的溶血嗜血杆菌，表明微量营养素的可用性，特别是铁，在这些物种的进化生态学中很重要。总的来说,我们的研究证明了metapangenomics识别可能影响微生物群落内生态相互作用的因素的力量，包括基因组多样性，栖息地专业化，和代谢多功能性。
目的：了解口腔的微生物生态学对于理解人体生理至关重要。这项研究采用了metapangenomics来揭示各种嗜血杆菌和Aggregatibacter物种在健康个体的口腔内表现出不同的生态偏好。从而支持站点专家假设。此外,观察到不同嗜血杆菌物种的基因库与其生态位相关。这些发现揭示了关键代谢功能在塑造口腔生态系统中微生物分布模式和种间相互作用中的重要性。
目的：了解口腔的微生物生态学对于理解人体生理至关重要。这项研究采用了metapangenomics来揭示各种嗜血杆菌和Aggregatibacter物种在健康个体的口腔内表现出不同的生态偏好。从而支持站点专家假设。此外,观察到不同嗜血杆菌物种的基因库与其生态位相关。这些发现揭示了关键代谢功能在塑造口腔生态系统中微生物分布模式和种间相互作用中的重要性。
