Microbial ecosystems are ubiquitous, populating virtually every place on earth. These communities are constituted by a wide range of microorganisms, including bacteria, archaea, viruses, fungi, and many other microscopic eukaryotes such as protists and protozoa. Together, they interact, cooperate, or compete to form highly dynamic and complex microbial communities in humans, animals, plants, or within the environment.

In the last two decades, the development of next-generation-sequencing technologies coupled with complementary multi-omics approaches and powerful analytic tools have led to the genesis of the Microbiome field. At the crossroads of many disciplines, including genomics, bioinformatics, evolution, ecology, molecular microbiology, and many more, microbiome research focuses on understanding the composition and function of microbial ecosystems. This is achieved through the identification and characterization of species and genes found within specific niches to further define the biological bases that underly microorganism–environment interactions. Therefore, this broad research field has many translational applications and the potential to meet many of the current and upcoming biomedical and environmental challenges faced by mankind.

In this special issue of Molecular Microbiology, we compiled an outstanding collection of papers from leaders in the field that report important findings and discuss emerging methods and concepts regarding the Molecular Microbiology of Microbiomes.

Among the major challenges, human health is obviously ranked highly and, in that context, studying the human gut microbiome has been a top priority. Indeed, several studies published in Molecular Microbiology and elsewhere have dissected the spatiotemporal composition and evolution of human gut microbiomes according to age, gender, ethnicity, dietary regime, or lifestyle and further reported how such parameters might be involved in cancer, obesity, or immunity.

At the early stages of our lives, microorganisms from maternal and environmental sources colonize the gastrointestinal tract. In their review, Melki and Litvak discuss how these dynamic microbiota communities evolve and play important roles in both infant and adult health (Melki and Litvak 2024). Although such studies have often focused on the large intestine, Shealy and colleagues remind us that the small intestine remains an understudied, yet equally important, gut niche that plays a critical role in the establishment of infectious and noninfectious diseases of the gastrointestinal tract (Shealy, Baltagulov, and Byndloss 2024). Changes in microbiota composition, especially in beneficial commensal microbes, can tip the balance from health to disease. Hence, identifying the factors and the respective biological processes by which commensals impact communities in the gastrointestinal tract is essential. Demiturk et al. discuss how the composition of the mucus layer, and more precisely its glycosylation state, contributes to maintaining cellular and microbial homeostasis in the gut and thus preventing disease (Demirturk, Cinar, and Avci 2024).

Because of their impact on the commensal communities, therapeutic or prophylactic treatment with broad-spectrum antibiotics can have deleterious effects on human and animal microbiomes. However, the effect of nonantimicrobial drugs on microbiomes has only recently started to be investigated. The work from Escalante and colleagues in this issue has described how the lipid-lowering anti-obesity drug simvastatin affects microbiota composition and the bacterial cell envelope profiles (Escalante et al. 2024). Two complementary studies by Cabirol et al. and Gonzalez et al. show that the composition and the subsequent interactions between the microbiota and host cells have the potential for tremendous effects on brain function, behavior, and also lifespan (Cabirol, Moriano-Gutierrez, and Engel 2024; Gonzalez and Irazoqui 2024).

From a One-Health perspective, with the continuous goal of benefiting human health, research on microbiomes is also essential to better understand how our human bodies interact with each other's, animals, and with our environment. In their study, Effelsberg et al. developed an experimental scheme for the temporal analysis of pig nasal microbiota dynamics that can be used for work toward preventing Methicillin-resistant Staphylococcus aureus (MRSA) transmission from animals to humans (Effelsberg et al. 2024). Then, Martinez-Perez and colleagues review our current knowledge on the role of space and proximity in phytoplankton–bacterial interactions, before discussing how a complete picture of such mechanisms might help to better predict ecological consequences on global elemental cycles (Martinez-Perez et al. 2024).

Analyzing and understanding ecosystems' dynamics at multiple scales has constituted an important stepping stone to further engineer and/or modulate microbiomes. Two studies published in this issue elegantly discuss the two major strategies commonly developed to achieve this ambitious objective. In the first study, Sànchez et al. describe how rational environmental manipulations can lead to the optimization of microbial functions and thus optimize microbial-based processes (Sanchez et al. 2024). In the second study, Dorado-Morales and colleagues highlight how conjugation can be used as a powerful tool to modify the microbiome by either editing the genome of specific bacterial species and/or the removal of certain taxonomic groups (Dorado-Morales, Lamberioux, and Mazel 2024).

We hope that this issue will be appreciated by the broad readership of our journal and further encourage our past, present, and future contributors to consider Molecular Microbiology for publishing their next high-level scientific stories.

微生物生态系统无处不在，几乎遍布地球上的每个地方。这些群落由多种微生物构成，包括细菌、古细菌、病毒、真菌和许多其他微观真核生物，如原生生物和原生动物。它们一起相互作用、合作或竞争，在人类、动物、植物或环境中形成高度动态和复杂的微生物群落。

在过去的二十年里，新一代测序技术的发展，加上互补的多组学方法和强大的分析工具，促成了微生物组领域的诞生。在基因组学、生物信息学、进化论、生态学、分子微生物学等许多学科的十字路口，微生物组研究侧重于了解微生物生态系统的组成和功能。这是通过鉴定和表征在特定生态位中发现的物种和基因来实现的，以进一步定义微生物-环境相互作用的生物基础。因此，这个广阔的研究领域具有许多转化应用，并有可能应对人类当前和即将到来的许多生物医学和环境挑战。

在本期《分子微生物学》特刊中，我们汇编了来自该领域领导者的杰出论文集，这些论文报告了重要发现并讨论了有关微生物组分子微生物学的新兴方法和概念。

在主要挑战中，人类健康显然排名靠前，在这种情况下，研究人类肠道微生物组一直是重中之重。事实上，发表在《分子微生物学》和其他地方的几项研究已经根据年龄、性别、种族、饮食习惯或生活方式剖析了人类肠道微生物组的时空组成和进化，并进一步报告了这些参数如何与癌症、肥胖或免疫有关。

在我们生命的早期阶段，来自母体和环境来源的微生物会在胃肠道中定植。在他们的评论中，Melki 和 Litvak 讨论了这些动态微生物群落如何进化并在婴儿和成人健康中发挥重要作用（Melki 和 Litvak 2024）。尽管此类研究通常集中在大肠上，但 Shealy 及其同事提醒我们，小肠仍然是一个研究不足但同样重要的肠道生态位，它在胃肠道感染性和非感染性疾病的建立中起着关键作用（Shealy、Baltagulov 和 Byndloss 2024）。微生物群组成的变化，尤其是有益共生微生物的变化，会使天平从健康转向疾病。因此，确定共生体影响胃肠道群落的因素和各自的生物过程至关重要。Demiturk 等人讨论了粘液层的组成，更准确地说是其糖基化状态，如何有助于维持肠道中的细胞和微生物稳态，从而预防疾病（Demirturk、Cinar 和 Avci 2024）。

由于广谱抗生素对共生群落的影响，广谱抗生素的治疗或预防性治疗会对人类和动物微生物组产生有害影响。然而，非抗菌药物对微生物组的影响直到最近才开始研究。Escalante 及其同事在本期中的工作描述了降脂抗肥胖药物辛伐他汀如何影响微生物群组成和细菌细胞包膜谱（Escalante 等人，2024 年）。Cabirol 等人和 Gonzalez 等人的两项互补研究表明，微生物群和宿主细胞之间的组成和随后的相互作用有可能对大脑功能、行为和寿命产生巨大影响（Cabirol、Moriano-Gutierrez 和 Engel 2024;Gonzalez 和 Irazoqui 2024）。

从 One-Health 的角度来看，为了造福人类健康，微生物组的研究对于更好地了解我们的人体如何与他人、动物以及我们的环境相互作用也至关重要。在他们的研究中，Effelsberg 等人开发了一种实验方案，用于对猪鼻微生物群动力学进行时间分析，可用于防止耐甲氧西林金黄色葡萄球菌 （MRSA） 从动物传播到人类（Effelsberg 等人，2024 年）。然后，Martinez-Perez 及其同事回顾了我们目前关于空间和邻近性在浮游植物-细菌相互作用中的作用的知识，然后讨论了此类机制的完整图景如何帮助更好地预测对全球元素循环的生态后果（Martinez-Perez 等人，2024 年）。

在多个尺度上分析和理解生态系统的动态构成了进一步设计和/或调节微生物组的重要垫脚石。本期发表的两项研究优雅地讨论了为实现这一雄心勃勃的目标而制定的两种常见策略。在第一项研究中，Sànchez 等人描述了合理的环境操纵如何导致微生物功能的优化，从而优化基于微生物的过程（Sanchez 等人，2024 年）。在第二项研究中，Dorado-Morales 及其同事强调了如何通过编辑特定细菌物种的基因组和/或去除某些分类组（Dorado-Morales、Lamberioux 和 Mazel 2024）将偶联用作改变微生物组的强大工具。

我们希望本期杂志的广泛读者能够欣赏本期杂志，并进一步鼓励我们过去、现在和未来的撰稿人考虑在《分子微生物学》上发表他们的下一个高水平科学故事。