Commensal microbe regulation of skin cells in disease.

Human skin is the host to various commensal microbes that constitute a substantial microbial community. The reciprocal communication between these microbial inhabitants and host cells upholds both the morphological and functional attributes of the skin layers, contributing indispensably to microenvironmental and tissue homeostasis. Thus, disruption of the skin barrier or imbalances in the microbial communities can exert profound effects on the behavior of host cells. This influence, mediated by the microbes themselves or their metabolites, manifests in diverse outcomes. In this review, we examine existing knowledge to provide insight into the nuanced behavior exhibited by the microbiota on skin cells in health and disease states. These interactions provide insight into potential cellular targets for future microbiota-based therapies to prevent and treat skin disease.

AI in microbiome research: Where have we been, where are we going?

Artificial intelligence (AI), a subdiscipline of computer science that develops machines or software that mimic characteristically human cognitive functions, is currently undergoing a revolution. In this commentary article, I will give my perspective on the evolution of the field and my thoughts on how AI may impact microbiome research in the next decade.

Synthetic microbial communities: A gateway to understanding resistance, resilience, and functionality in spontaneously fermented food microbiomes.

This review delves into the intricate traits of microbial communities encountered in spontaneously fermented foods (SFF), contributing to resistance, resilience, and functionality drivers. Traits of SFF microbiomes comprise of fluctuations in community composition, genetic stability, and condition-specific phenotypes. Synthetic microbial communities (SMCs) serve as a portal for mechanistic insights and strategic re-programming of microbial communities. Current literature underscores the pivotal role of microbiomes in SFF in shaping quality attributes and preserving the cultural heritage of their origin. In contrast to starter driven fermentations that tend to be more controlled but lacking the capacity to maintain or reproduce the complex flavors and intricacies found in SFF. SMCs, therefore, become indispensable tools, providing a nuanced understanding and control over fermented food microbiomes. They empower the prediction and engineering of microbial interactions and metabolic pathways with the aim of optimizing outcomes in food processing. Summarizing the current application of SMCs in fermented foods, there is still space for improvement. Challenges in achieving stability and reproducibility in SMCs are identified, stemming from non-standardized approaches. The future direction should involve embracing standardized protocols, advanced monitoring tools, and synthetic biology applications. A holistic, multi-disciplinary approach is paramount to unleashing the full potential of SMCs and fostering sustainable and innovative applications in fermented food systems.

The impact of raw material form and starter culture inoculation on bacterial communities and metabolites in fermented anchovy sauce.

This study explored the dynamics of anchovy sauce fermentation and investigated how the raw material form and the use of starter cultures affect bacterial and metabolite profiles. Using a comprehensive approach, we examined the fermentation process using anchovies in two forms (whole and ground) and three different starter cultures. The use of ground anchovies resulted in an accelerated fermentation process for anchovy sauce; however, the increased diversity of bacterial phylotypes and altered accumulation of biogenic amines were observed. Inoculation of starter cultures resulted in a shift from spontaneous to controlled fermentation, highlighting their ability to regulate bacterial communities. Despite a slightly reduced fermentation rate, inoculation with Tetragenococcus halophilus was shown to be a potent method for reducing biogenic amines and affecting metabolite profiles. As the industry strives to balance fermentation speed and quality, our research could provide insights for improving the efficiency, safety, and quality of anchovy sauce production.

Nutrient and moisture limitations reveal keystone metabolites linking rhizosphere metabolomes and microbiomes.

Plants release a wealth of metabolites into the rhizosphere that can shape the composition and activity of microbial communities in response to environmental stress. The connection between rhizodeposition and rhizosphere microbiome succession has been suggested, particularly under environmental stress conditions, yet definitive evidence is scarce. In this study, we investigated the relationship between rhizosphere chemistry, microbiome dynamics, and abiotic stress in the bioenergy crop switchgrass grown in a marginal soil under nutrient-limited, moisture-limited, and nitrogen (N)-replete, phosphorus (P)-replete, and NP-replete conditions. We combined 16S rRNA amplicon sequencing and LC-MS/MS-based metabolomics to link rhizosphere microbial communities and metabolites. We identified significant changes in rhizosphere metabolite profiles in response to abiotic stress and linked them to changes in microbial communities using network analysis. N-limitation amplified the abundance of aromatic acids, pentoses, and their derivatives in the rhizosphere, and their enhanced availability was linked to the abundance of bacterial lineages from Acidobacteria, Verrucomicrobia, Planctomycetes, and Alphaproteobacteria. Conversely, N-amended conditions increased the availability of N-rich rhizosphere compounds, which coincided with proliferation of Actinobacteria. Treatments with contrasting N availability differed greatly in the abundance of potential keystone metabolites; serotonin and ectoine were particularly abundant in N-replete soils, while chlorogenic, cinnamic, and glucuronic acids were enriched in N-limited soils. Serotonin, the keystone metabolite we identified with the largest number of links to microbial taxa, significantly affected root architecture and growth of rhizosphere microorganisms, highlighting its potential to shape microbial community and mediate rhizosphere plant-microbe interactions.

The clinical impacts of lung microbiome in bronchiectasis with fixed airflow obstruction: a prospective cohort study.

BACKGROUND: Airflow obstruction is a hallmark of disease severity and prognosis in bronchiectasis. The relationship between lung microbiota, airway inflammation, and outcomes in bronchiectasis with fixed airflow obstruction (FAO) remains unclear. This study explores these interactions in bronchiectasis patients, with and without FAO, and compares them to those diagnosed with chronic obstructive pulmonary disease (COPD). METHODS: This prospective observational study in Taiwan enrolled patients with either bronchiectasis or COPD. To analyze the lung microbiome and assess inflammatory markers, bronchoalveolar lavage (BAL) samples were collected for 16S rRNA gene sequencing. The study cohort comprised 181 patients: 86 with COPD, 46 with bronchiectasis, and 49 with bronchiectasis and FAO, as confirmed by spirometry. RESULTS: Patients with bronchiectasis, with or without FAO, had similar microbiome profiles characterized by reduced alpha diversity and a predominance of Proteobacteria, distinctly different from COPD patients who exhibited more Firmicutes, greater diversity, and more commensal taxa. Furthermore, compared to COPD and bronchiectasis without FAO, bronchiectasis with FAO showed more severe disease and a higher risk of exacerbations. A significant correlation was found between the presence of Pseudomonas aeruginosa and increased airway neutrophilic inflammation such as Interleukin [IL]-1ß, IL-8, and tumor necrosis factor-alpha [TNF]-α, as well as with higher bronchiectasis severity, which might contribute to an increased risk of exacerbations. Moreover, in bronchiectasis patients with FAO, the ROSE (Radiology, Obstruction, Symptoms, and Exposure) criteria were employed to classify individuals as either ROSE (+) or ROSE (-), based on smoking history. This classification highlighted differences in clinical features, inflammatory profiles, and slight microbiome variations between ROSE (-) and ROSE (+) patients, suggesting diverse endotypes within the bronchiectasis with FAO group. CONCLUSION: Bronchiectasis patients with FAO may exhibit two distinct endotypes, as defined by ROSE criteria, characterized by greater disease severity and a lung microbiome more similar to bronchiectasis without FAO than to COPD. The significant correlation between Pseudomonas aeruginosa colonization and increased airway neutrophilic inflammation, as well as disease severity, underscores the clinical relevance of microbial patterns. This finding reinforces the potential role of these patterns in the progression and exacerbations of bronchiectasis with FAO.

The impact of filamentous plant pathogens on the host microbiota.

When a pathogen invades a plant, it encounters a diverse microbiota with some members contributing to the health and growth of the plant host. So far, the relevance of interactions between pathogens and the plant microbiota are poorly understood; however, new lines of evidence suggest that pathogens play an important role in shaping the microbiome of their host during invasion. This review aims to summarize recent findings that document changes in microbial community composition during the invasion of filamentous pathogens in plant tissues. We explore the known mechanisms of interaction between plant pathogens and the host microbiota that underlie these changes, particularly the pathogen-encoded traits that are produced to target specific microbes. Moreover, we discuss the limitations of current strategies and shed light on new perspectives to study the complex interaction networks between filamentous pathogens and the plant microbiome.

A novel strategy of artificially regulating plant rhizosphere microbial community to promote plant tolerance to cold stress.

Artificial regulation of plant rhizosphere microbial communities through the synthesis of microbial communities is one of the effective ways to improve plant stress resistance. However, the process of synthesizing stress resistant microbial communities with excellent performance is complex, time-consuming, and costly. To address this issue, we proposed a novel strategy for preparing functional microbial communities. We isolated a cultivable cold tolerant bacterial community (PRCBC) from the rhizosphere of peas, and studied its effectiveness in assisting rice to resist stress. The results indicate that PRCBC can not only improve the ability of rice to resist cold stress, but also promote the increase of rice yield after cold stress relieved. This is partly because PRCBC increases the nitrogen content in the rhizosphere soil, and promotes rice's absorption of nitrogen elements, thereby promoting rice growth and enhancing its ability to resist osmotic stress. More importantly, the application of PRCBC drives the succession of rice rhizosphere microbial communities, and promotes the succession of rice rhizosphere microbial communities towards stress resistance. Surprisingly, PRCBC drives the succession of rice rhizosphere microbial communities towards a composition similar to PRCBC. This provides a feasible novel method for artificially and directionally driving microbial succession. In summary, we not only proposed a novel and efficient strategy for preparing stress resistant microbial communities to promote plant stress resistance, but also unexpectedly discovered a possible directionally driving method for soil microbial community succession.

Enhanced metabolic entanglement emerges during the evolution of an interkingdom microbial community.

While different stages of mutualism can be observed in natural communities, the dynamics and mechanisms underlying the gradual erosion of independence of the initially autonomous organisms are not yet fully understood. In this study, by conducting the laboratory evolution on an engineered microbial community, we reproduce and molecularly track the stepwise progression towards enhanced partner entanglement. We observe that the evolution of the community both strengthens the existing metabolic interactions and leads to the emergence of de novo interdependence between partners for nitrogen metabolism, which is a common feature of natural symbiotic interactions. Selection for enhanced metabolic entanglement during the community evolution repeatedly occurred indirectly, via pleiotropies and trade-offs within cellular regulatory networks, and with no evidence of group selection. The indirect positive selection of metabolic dependencies between microbial community members, which results from the direct selection of other coupled traits in the same regulatory network, may therefore be a common but underappreciated driving force guiding the evolution of natural mutualistic communities.

Does the oral microbiota evolve differently during orthodontic treatment with vestibular multi-attachment fixed appliances versus aligners? A systematic review of the literature / Est-ce que le microbiote oral évolue différemment lors d'un traitement orthodontique par appareil fixe multi-attache vestibulaire versus par aligneurs ? Une revue systématique de la littérature.

Introduction: Oral microbiota of patients is impacted during orthodontic treatment. The objective of this systematic review was to observe the evolution of oral microbiota (primary objective) and periodontal health (secondary objective) during orthodontic treatment, and to compare these changes during treatment with vestibular fixed appliances and aligners. Materials and Methods: In accordance with PRISMA guidelines, an electronic search was performed in four databases until January 2022, completed by a manual search, including all prospective controlled studies, randomized or not, on the subject. Two independent authors were involved in the selection of studies, and a third author was consulted in case of disagreement. The Cochrane Collaboration's tool and ROBINS-I tool was used to assess the risk-of-bias in randomized and non-randomized trials, respectively. Finally, the risk of bias graphs were made with the robvis visualization tool. Results: Out of the 994 results obtained from these searches, 11 eligible articles were included (4 randomized clinical trials and 7 non-randomized controlled studies) with varying levels of bias. Results suggested that patients treated with aligner appliances have more favorable microbial flora and less biofilm mass during their treatment compared with those treated with fixed appliances. In addition, inflammatory marker cytokines and periodontal indices were higher in fixed orthodontic treatment compared to aligners treatment. Conclusion: Considering the limitations of this systematic review of the literature, the results suggested that aligners have a more favorable impact on the oral microbiota and periodontium compared to vestibular fixed appliances. PROSPERO registration: CRD42022276486.

Introduction: Il est désormais reconnu que le microbiote oral des patients est impacté au cours du traitement orthodontique. L'objectif de cette revue systématique était d'observer l'évolution du microbiote oral (objectif principal) et de la santé parodontale (objectif secondaire) lors du traitement orthodontique, et de comparer ces modifications lors du traitement par appareils multi-attaches vestibulaires et par aligneurs. Matériels et méthodes: Conformément aux directives PRISMA, une recherche électronique a été réalisée dans quatre bases de données jusqu'à janvier 2022, complétée par une recherche manuelle, incluant toutes les études prospectives contrôlées, randomisées ou non, sur le sujet. Deux auteurs indépendants ont été impliqués dans la sélection des études et un troisième auteur a été sollicité en cas de désaccord. L'outil The Cochrane Collaboration's tool et l'outil ROBINS-I ont été utilisés pour évaluer le risque de biais dans les essais randomisés et non randomisés, respectivement. Finalement, les graphiques des risques de biais ont été réalisés avec l'outil robvis. Résultats: Parmi les 994 résultats issus de ces recherches, onze articles éligibles ont été inclus, comprenant quatre essais cliniques randomisés et sept études contrôlées non randomisées, avec des niveaux de biais variables. Les résultats suggèrent que les patients traités par gouttières orthodontiques présentent une flore microbienne plus favorable, ainsi qu'une masse de biofilm moins élevée au cours du traitement par rapport à ceux traités par appareils fixes multi-attaches. De plus, les cytokines marqueuses d'inflammation et les indices parodontaux étaient plus importants lors des traitements orthodontiques par appareils multi-attaches. Conclusion: Tenant compte des limites associées à cette revue systématique de la littérature, les résultats semblent suggérer que les aligneurs ont un impact plus favorable sur le microbiote oral et sur le parodonte que les appareils fixes multi-attaches. Enregistrement PROSPERO : CRD42022276486.

The Human Microbiome-A Physiologic Perspective.

The human microbiome consists of the microorganisms associated with the body, such as bacteria, fungi, archaea, protozoa, and viruses, along with their gene content and products. These microbes are abundant in the digestive, respiratory, renal/urinary, and reproductive systems. While microbes found in other organs/tissues are often associated with diseases, some reports suggest their presence even in healthy individuals. Lack of microbial colonization does not indicate a lack of microbial influence, as their metabolites can affect distant locations through circulation. In a healthy state, these microbes maintain a mutualistic relationship and help shape the host's physiological functions. Unlike the host's genetic content, microbial gene content and expression are dynamic and influenced by factors such as ethnicity, genetic background, sex, age, lifestyle/diet, and psychological/physical conditions. Therefore, defining a healthy microbiome becomes challenging as it is context dependent and can vary over time for an individual. Although differences in microbial composition have been observed in various diseases, these changes may reflect host alterations rather than causing the disease itself. As the field is evolving, there is increased emphasis on understanding when changes in the microbiome are an important component of pathogenesis rather than the consequence of a disease state. This article focuses on the microbial component in the digestive and respiratory tracts-the primary sites colonized by microorganisms-and the physiological functions of microbial metabolites in these systems. It also discusses their physiological functions in the central nervous and cardiovascular systems, which have no microorganism colonization under healthy conditions based on human studies. © 2024 American Physiological Society. Compr Physiol 14:5491-5519, 2024.

Interactions Between Oral Microbiota and Cancers in the Aging Community: A Narrative Review.

The oral microbiome potentially wields significant influence in the development of cancer. Within the human oral cavity, an impressive diversity of more than 700 bacterial species resides, making it the second most varied microbiome in the body. This finely balanced oral microbiome ecosystem is vital for sustaining oral health. However, disruptions in this equilibrium, often brought about by dietary habits and inadequate oral hygiene, can result in various oral ailments like periodontitis, cavities, gingivitis, and even oral cancer. There is compelling evidence that the oral microbiome is linked to several types of cancer, including oral, pancreatic, colorectal, lung, gastric, and head and neck cancers. This review discussed the critical connections between cancer and members of the human oral microbiota. Extensive searches were conducted across the Web of Science, Scopus, and PubMed databases to provide an up-to-date overview of our understanding of the oral microbiota's role in various human cancers. By understanding the possible microbial origins of carcinogenesis, healthcare professionals can diagnose neoplastic diseases earlier and design treatments accordingly.

Interactions between oral microbiota shifts and cancer: The oral microbiome potentially wields significant influence in the development of cancer. Within the human oral cavity, an impressive diversity of more than 700 bacterial species resides, making it the second most varied microbiome in the body. This finely balanced oral microbiome ecosystem is vital for sustaining oral health. However, disruptions in this equilibrium, often brought about by dietary habits and inadequate oral hygiene, can result in various oral ailments like periodontitis, cavities, gingivitis, and even oral cancer. There is compelling evidence that the oral microbiome is linked to several types of cancer, including oral, pancreatic, colorectal, lung, gastric, and head and neck cancers. This review discussed the critical connections between cancer and members of the human oral microbiota. Extensive searches were conducted across the Web of Science, Scopus, and PubMed databases to provide an up-to-date overview of our understanding of the oral microbiota's role in various human cancers. By understanding the possible microbial origins of carcinogenesis, healthcare professionals can diagnose neoplastic diseases earlier and design treatments accordingly.

Microbial interactions in mixed-species biofilms on the surfaces of Baijiu brewing environments.

Environmental microorganisms commonly inhabit dense multispecies biofilms, fostering mutualistic relationships and co-evolution. However, the mechanisms underlying biofilm formation and microbial interactions within the Baijiu fermentation microecosystem remain poorly understood. Hence, the objective of this study was to investigate the composition, structure, and interactions of microorganisms residing in biofilms on environmental surfaces in Baijiu production. The results revealed a shift in the bacteria-fungi interaction network following fermentation, transitioning from a cooperative/symbiotic relationship to a competitive/antagonistic dynamic. Core microbiota within the biofilms comprised lactic acid bacteria (LAB), yeast, and filamentous fungi. From the environmental surface samples, we isolated two strains of LAB (Lactiplantibacillus pentosus EB27 and Pediococcus pentosaceus EB35) and one strain of yeast (Pichia kudriavzevii EF8), all displaying remarkable biofilm formation and fermentation potential. Co-culturing LAB and yeast demonstrated a superior capacity for dual-species biofilm formation compared to mono-species biofilms. The dual-species biofilm displayed a two-layer structure, with LAB in the lower layer and serving as the foundation for the yeast community in the upper layer. The upper layer exhibited a dense distribution of yeast, enhancing aerobic respiration. Metabolic activities in the dual-species biofilm, such as ABC transporter, oxidative phosphorylation, citric acid cycle, sulfur metabolism, glycine, serine, threonine metabolism, lysine degradation, and cysteine and methionine metabolism, showed significant alterations compared to LAB mono-species biofilms. Moreover, bacterial chemotaxis, starch, and sucrose metabolism in the dual-species biofilm exhibited distinct patterns from those observed in the yeast mono-species biofilm. This study demonstrated that a core microbiota with fermentation potential may exist in the form of a biofilm on the surface of a Baijiu brewing environment. These findings provide a novel strategy for employing synthetic stable microbiotas in the intelligent brewing of Baijiu.

Shaping Microbiota During the First 1000 Days of Life.

Given that the host-microbe interaction is shaped by the immune system response, it is important to understand the key immune system-microbiota relationship during the period from conception to the first years of life. The present work summarizes the available evidence concerning human reproductive microbiota, and also, the microbial colonization during early life, focusing on the potential impact on infant development and health outcomes. Furthermore, we conclude that some dietary strategies including specific probiotics and other-biotics could become potentially valuable tools to modulate the maternal-neonatal microbiota during this early critical window of opportunity for targeted health outcomes throughout the entire lifespan.

The hidden link: How oral and respiratory microbiomes affect multiple sclerosis.

BACKGROUND: Extensive research has explored the role of gut microbiota in multiple sclerosis (MS). However, the impact of microbial communities in the oral cavity and respiratory tract on MS is an emerging area of investigation. PURPOSE: We aimed to review the current literature related to the nasal, oral, and lung microbiota in people with MS (PwMS). METHODS: We conducted a narrative review of clinical and preclinical original studies on PubMed that explored the relationship between the bacterial or viral composition of the nasal, lung, and oral microbiota and MS. Additionally, to find relevant studies not retrieved initially, we also searched for references in related review papers, as well as the references cited within the included studies. RESULTS AND CONCLUSIONS: Thirteen studies were meticulously reviewed in three sections; oral microbiota (n = 8), nasal microbiota (n = 3), and lung microbiota (n = 2), highlighting considerable alterations in the oral and respiratory microbiome of PwMS compared to healthy controls (HCs). Genera like Aggregatibacter and Streptococcus were less abundant in the oral microbiota of PwMS compared to HCs, while Staphylococcus, Leptotrichia, Fusobacterium, and Bacteroides showed increased abundance in PwMS. Additionally, the presence of specific bacteria, including Streptococcus sanguinis, within the oral microbiota was suggested to influence Epstein-Barr virus reactivation, a well-established risk factor for MS. Studies related to the nasal microbiome indicated elevated levels of specific Staphylococcus aureus toxins, as well as nasal glial cell infection with human herpes virus (HHV)-6 in PwMS. Emerging research on lung microbiome in animal models demonstrated that manipulating the lung microbiome towards lipopolysaccharide-producing bacteria might suppress MS symptoms. These findings open avenues for potential therapeutic strategies. However, further research is crucial to fully understand the complex interactions between the microbiome and MS. This will help identify the most effective timing, bacterial strains, and modulation techniques.

Influence of the initial microbiota on eggplant shibazuke pickle and eggplant juice fermentation.

The present study aimed to investigate the effects of the initial microbiota on microbial succession and metabolite transition during eggplant fermentation. Samples of traditional Japanese eggplant pickles, shibazuke, which were spontaneously fermented by plant-associated microbiota, were used for the analysis. Microbiota analysis indicated two successional patterns: early dominance of lactic acid bacteria superseded by aerobic bacteria and early dominance of lactic acid bacteria maintained to the end of the production process. Next, shibazuke production was modeled using filter-sterilized eggplant juice, fermenting the average composition of the initial shibazuke microbiota, which was artificially constructed from six major species identified during shibazuke production. In contrast to shibazuke production, all batches of eggplant juice fermentation showed almost identical microbial succession and complete dominance of Lactiplantibacillus plantarum in the final microbiota. These findings revealed the fate of initial microbiota under shibazuke production conditions: the early dominance of lactic acid bacteria that was maintained throughout, with L. plantarum ultimately predominating the microbiota. Furthermore, a comparison of the results between shibazuke production and eggplant juice fermentation suggested that L. plantarum is involved in the production of lactic acid, alanine, and glutamic acid during eggplant fermentation regardless of the final microbiota. IMPORTANCE: The findings shown in this study provide insight into the microbial succession during spontaneous pickle fermentation and the role of Lactiplantibacillus plantarum in eggplant pickle production. Moreover, the novel method of using filter-sterilized vegetable juice with an artificial microbiota to emulate spontaneous fermentation can be applied to other spontaneously fermented products. This approach allows for the evaluation of the effect of specific initial microbiota in the absence of plant-associated bacteria from raw materials potentially promoting a greater understanding of microbial behavior in complex microbial ecosystems during vegetable fermentation.

Unearthing the power of microbes as plant microbiome for sustainable agriculture.

In recent years, research into the complex interactions and crosstalk between plants and their associated microbiota, collectively known as the plant microbiome has revealed the pivotal role of microbial communities for promoting plant growth and health. Plants have evolved intricate relationships with a diverse array of microorganisms inhabiting their roots, leaves, and other plant tissues. This microbiota mainly includes bacteria, archaea, fungi, protozoans, and viruses, forming a dynamic and interconnected network within and around the plant. Through mutualistic or cooperative interactions, these microbes contribute to various aspects of plant health and development. The direct mechanisms of the plant microbiome include the enhancement of plant growth and development through nutrient acquisition. Microbes have the ability to solubilize essential minerals, fix atmospheric nitrogen, and convert organic matter into accessible forms, thereby augmenting the nutrient pool available to the plant. Additionally, the microbiome helps plants to withstand biotic and abiotic stresses, such as pathogen attacks and adverse environmental conditions, by priming the plant's immune responses, antagonizing phytopathogens, and improving stress tolerance. Furthermore, the plant microbiome plays a vital role in phytohormone regulation, facilitating hormonal balance within the plant. This regulation influences various growth processes, including root development, flowering, and fruiting. Microbial communities can also produce secondary metabolites, which directly or indirectly promote plant growth, development, and health. Understanding the functional potential of the plant microbiome has led to innovative agricultural practices, such as microbiome-based biofertilizers and biopesticides, which harness the power of beneficial microorganisms to enhance crop yields while reducing the dependency on chemical inputs. In the present review, we discuss and highlight research gaps regarding the plant microbiome and how the plant microbiome can be used as a source of single and synthetic bioinoculants for plant growth and health.

Impact of host species on assembly, composition, and functional profiles of phycosphere microbiomes.

Microalgal microbiomes play vital roles in the growth and health of their host, however, their composition and functions remain only partially characterized, especially across microalgal phyla. In this study, a natural seawater microbiome was introduced to three distinct, axenic species of microalgae, the haptophyte Isochrysis galbana, the chlorophyte Tetraselmis suecica, and the diatom Conticribra weissflogii (previously Thalassiosira), and its divergence and assembly under constant illumination was monitored over 49 days using 16S rRNA amplicon and metagenomic analyses. The microbiomes had a high degree of host specificity in terms of taxonomic composition and potential functions, including CAZymes profiles. Rhodobacteraceae and Flavobacteriaceae families were abundant across all microalgal hosts, but I. galbana microbiomes diverged further from T. suecica and C. weissflogii microbiomes. I. galbana microbiomes had a much higher relative abundance of Flavobacteriaceae, whereas the two other algal microbiomes had higher relative abundances of Rhodobacteraceae. This could be due to the bacterivorous mixotrophic nature of I. galbana affecting the carbohydrate composition available to the microbiomes, which was supported by the CAZymes profile of I. galbana microbiomes diverging further from those of T. suecica and C. weissflogii microbiomes. Finally, the presence of denitrification and other anaerobic pathways was found exclusively in the microbiomes of C. weissflogii, which we speculate could be a result of anoxic microenvironments forming in aggregates formed by this diatom during the experiment. These results underline the significant role of the microalgal host species on microbiome composition and functional profiles along with other factors, such as the trophic mode of the microalgal host. IMPORTANCE: As the main primary producers of the oceans, microalgae serve as cornerstones of the ecosystems they are part of. Additionally, they are increasingly used for biotechnological purposes such as the production of nutraceuticals, pigments, and antioxidants. Since the bacterial microbiomes of microalgae can affect their hosts in beneficial and detrimental ways, understanding these microbiomes is crucial to both the ecological and applied roles of microalgae. The present study advances the understanding of microalgal microbiome assembly, composition, and functionality across microalgal phyla, which may inform the modeling and engineering of microalgal microbiomes for biotechnological purposes.

Sphingomonas sp. Hbc-6 alters Arabidopsis metabolites to improve plant growth and drought resistance by manipulating the microbiome.

Drought significantly affects crop productivity and poses a considerable threat to agricultural ecosystems. Plant growth-promoting bacteria (PGPB) and plant microbiome play important roles in improving drought resistance and plant performance. However, the response of the rhizosphere microbiota to PGPB during the development of plants and the interaction between inoculum, microbiota, and plants under drought stress remain to be explored. In the present study, we used culturomic, microbiomic, and metabonomic analyses to uncover the mechanisms by which Sphingomonas sp. Hbc-6, a PGPB, promotes Arabidopsis growth and enhances drought resistance. We found that the rhizosphere microbiome assembly was interactively influenced by developmental stage, Hbc-6, and drought; the bacterial composition exhibited three patterns of shifts with developmental stage: resilience, increase, and decrease. Drought diminished microbial diversity and richness, whereas Hbc-6 increased microbial diversity and helped plants recruit specific beneficial bacterial taxa at each developmental stage, particularly during the bolting stage. Some microorganisms enriched by Hbc-6 had the potential to promote carbon and nitrogen cycling processes, and 86.79 % of the isolated strains exhibited PGP characteristics (for example Pseudomonas sp. TA9). They jointly regulated plant physiological metabolism (i.e., upregulated drought resistant-facilitating substances and reduced harmful substances), thereby stimulating the growth of Arabidopsis and increasing plant biomass under drought stress conditions. Collectively, these results indicate that Hbc-6 mediates plant growth and drought resistance by affecting the microbiome. The study thus provides novel insights and strain resources for drought-resistant, high-yielding crop cultivation and breeding.