Microbial Species Composition Research Articles

Analysis of the composition and function of rhizosphere microbial communities in plants with tobacco bacterial wilt disease and healthy plants

ABSTRACT To explore the factors influencing the occurrence of bacterial wilt, the differences in the physicochemical properties, microbial community composition and function between rhizosphere soil of tobacco plants with bacterial wilt and healthy plants in the tobacco planting area of Fuzhou City, Jiangxi Province were analyzed and compared. The results showed that the rhizosphere soil of diseased tobacco exhibited significantly reduced levels of exchangeable potassium, water-soluble potassium, nitrate nitrogen, total nitrogen and pH, in comparison to the rhizosphere soil of healthy plants. Conversely, the available phosphorus content of the rhizosphere soil of diseased tobacco was significantly increased. The amount of Ralstonia solanacearum in soil was negatively correlated with pH, nitrate nitrogen and total nitrogen, and positively correlated with exchangeable potassium and water-soluble potassium. A total of 43 genera were significantly different between the two groups of rhizosphere soil, of which 24 genera were enriched in the rhizosphere of healthy plants, including Ideonella , Rhizophagus , Rhizobacter , Altererythrobacter and Ignavibacterium associated with plant disease resistance, Thermodesulfovibrio , Syntrophorhabdus , Syntrophus , Chlorobium , Hydrogenophaga and Limnohabitans associated with soil sulfur metabolism, as well as Ignavibacterium , Ideonella , Derxia and Azohydromonas associated with soil nitrogen cycling. Kyoto Encyclopedia of Genes and Genomes functional analysis of the unigenes obtained by metagenomic sequencing also showed that the differential unigenes were significantly enriched in the sulfur metabolism pathway. In addition, the rhizosphere soil of diseased tobacco plants exhibited a higher abundance of antibiotic-producing actinomycetes and an increased load of antibiotic resistance genes compared to that of healthy plants. In general, lower pH value, less content of nitrate nitrogen and total nitrogen, and more content of exchangeable potassium and water-soluble potassium could contribute to onset of bacterial wilt. Twenty-four genera, including Ideonella and Rhizophagus , may construct a healthy microecological network in the rhizosphere of tobacco plants. All these factors may interact with each other to control the development of bacterial wilt. This complicated interaction network needs to be explored further. IMPORTANCE Previous studies have mainly focused on the differences in microbial species composition between healthy and diseased soils, but the differences in microbial community functions between two types of soil have not been well characterized. In this study, soil samples in diseased and healthy plant rhizospheres were collected for physicochemical property testing and metagenomic sequencing. We focused on analyzing the differences in physicochemical properties and microbial community functions between these soils, as well as the correlation between these factors and pathogen content. The results of this study provide a theoretical basis for further understanding the occurrence of tobacco bacterial wilt in the field.

Effects of gradual increase of ciprofloxacin and cefotaxime on nitrogen and phosphorus removal and microbial community in moving bed biofilm reactor

To clarify the effects of trace amount of antibiotics in wastewater on biofilm reactor, this study explored the effects of gradual increase of ciprofloxacin (CIP) and cefotaxime (CTX) ranging from 100 to 1000 ng·L−1 on the nitrogen and phosphorus removal and microbial community in a moving bed biofilm reactor (MBBR). Under different phases of CIP and CTX gradual increase, the resilience of culturable functional bacteria including ammonifying bacteria, nitrite oxidizing bacteria, aerobic denitrifying bacteria and phosphorus accumulating organisms in the biofilm was analyzed. High-throughput sequencing analysis was used to reveal the microbial community structure and species composition of functional bacteria. The results indicated that the treatment performance of MBBR was temporarily affected by trace CIP and CTX and returned to its original level within 1–2 days. Ammonifying bacteria exhibited strong resilience in trace CIP and CTX stress environments. Trace CIP and CTX altered the microbial community structure in biofilm, but the performance of nitrogen and phosphorus removal in MBBR was slightly affected. This might attribute to the rapid proliferation of Thauera, Dechloromonas and Candidatus_Accumulibacter on the carrier biofilm. The research results help to deepen the understanding of the impact of trace antibiotics on the MBBR and to provide a reference for the development of microbial germplasm resources for biological nitrogen and phosphorus removal from wastewater under antibiotic stress conditions.

Elucidating biogeochemical characterization of nitrogen in the vadose zone integrating geochemistry, microorganism, and numerical simulation

A thorough comprehension of nitrogen biogeochemical processes in the vadose zone is crucial for the effective prevention and remediation of soil-groundwater system contamination. Despite the growing research on this subject, the full scope of nitrogen biogeochemical characterization in different geological environments remains poorly understood. This study addresses this knowledge gap by integrating geochemical, microbiological and numerical simulation approaches to gain a deeper insight into nitrogen biogeochemistry in agriculture. Our findings indicate the biogeochemical behavior of nitrogen in the vadose zone is mediated by microorganisms, driven by hydraulics, influenced by geological conditions and environmental factors. Along the groundwater flow, NH4+-N was found to be heavily accumulated in the topsoil of 0–40 cm, while NO3−-N was transported and driven by hydrodynamics from both vertical and horizontal directions. Microbial diversity, species composition and functional microorganisms were significantly influenced by soil depth, rather than geomorphological types. Oxidation-reduction potential (ORP), total organic carbon (TOC), soil moisture (MOI), bicarbonate (HCO3−), and ferrous (Fe2+) were identified as the principal environmental factors that regulate nitrogen metabolism and the dominant biochemical processes, encompassing nitrogen fixation, nitrification, and denitrification. Driven by hydrodynamics, NH4+-N, NO2−-N and NO3−-N tend to form distinct biochemical reaction zones in the vertical vadose zone. These areas are dynamic and subject to geomorphologies. It should be noted that NO3−-N can migrate towards groundwater from the clayey sand in the Alluvial Plain, which presents a potential risk of groundwater contamination. The fissure structure of loess may serve as the major transport pathway for groundwater nitrogen contamination in the Loess Tableland. This finding highlights the importance of integrating microbiology, geochemistry and hydraulics to elucidate the biogeochemical processes of nitrogen in the vadose zone with a dynamic mindset.

Multi-omics co-analysis of the differences in microbial species composition and function between spontaneous and inoculated wine fermentation must

Emphasize on natural wines has gained prominence in the wine industry. However, there is a lack of research on natural wines that are fermented relying solely on grape skin-resident microorganisms. The microbes in spontaneous and inoculated fermentation must were analyzed utilizing 16S ITS rRNA sequencing, metabolomics, and metagenomics. The upregulated primary metabolites involved in Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment pathways suggesting that the stress resistance of Saccharomyces was more robust and complex during spontaneous fermentation. Gene functional analysis indicated that Saccharomyces and non- Saccharomyces yeasts play crucial roles in carbohydrate metabolism, and their functions are complementary. The non- Saccharomyces yeasts contributed positively to the overall characteristics of the spontaneous wine. An analysis of the correlations between the dominant microorganisms and metabolites proved that more abundant strains participated in the fermentation of spontaneous wines and had a positive effect on the fermentation process of the wines.

A Journey into the Evolution of Human Host-Oral Microbiome Relationship through Ancient Dental Calculus: A Scoping Review.

One of the most promising areas of research in palaeomicrobiology is the study of the human microbiome. In particular, ancient dental calculus helps to reconstruct a substantial share of oral microbiome composition by mapping together human evolution with its state of health/oral disease. This review aims to trace microbial characteristics in ancient dental calculus to describe the evolution of the human host-oral microbiome relationship in oral health or disease in children and adults. Following the PRISMA-Extension for Scoping Reviews guidelines, the main scientific databases (PubMed, Scopus, Lilacs, Cochrane Library) have been drawn upon. Eligibility criteria were established, and all the data collected on a purpose-oriented collection form were analysed descriptively. From the initial 340 records, only 19 studies were deemed comprehensive enough for the purpose of this review. The knowledge of the composition of ancient oral microbiomes has broadened over the past few years thanks to increasingly well-performing decontamination protocols and additional analytical avenues. Above all, metagenomic sequencing, also implemented by state-of-the-art bioinformatics tools, allows for the determination of the qualitative-quantitative composition of microbial species associated with health status and caries/periodontal disease. Some microbial species, especially periodontal pathogens, do not appear to have changed in history, while others that support caries disease or oral health could be connected to human evolution through lifestyle and environmental contributing factors.

Research Progress on the Composition and Interaction of Microbes in Kombucha

Kombucha, a fermented beverage produced by a symbiotic culture system of bacteria and yeast (SCOBY), is rich in bioactive compounds, thereby exhibiting various health benefits. In recent years, kombucha has gained global popularity as a healthy fermented beverage, leading to an upsurge in worldwide research interest. The diversity of microbial communities and the interactions between microorganisms play a vital role in the formation of unique flavor and health benefits of kombucha. At present, they have aroused widespread research interest worldwide. This review systematically summarizes recent achievements in research on the microbial composition and interactions in kombucha fermentation. Firstly, the progress obtained on the microbial species identification and the characteristics of their composition of kombucha were summarized. Then, the current researches on the interactions of the native microorganisms in Kombucha SCOBY were presented, as well as the interactions between additional microorganisms and native microorganisms. Finally, the dynamic changes observed during kombucha fermentation, including microbial species composition and key active substances such as organic acids and polyphenols, were reviewed. This article aims to provide valuable reference for using targeted microbial regulation to enhance the fermentation efficiency, and optimize product quality and efficacy of kombucha.

Exploring the microbial ecosystem of Berchemia polyphylla var. leioclada: a comprehensive analysis of endophytes and rhizospheric soil microorganisms.

Endophytic and rhizospheric microorganisms associated with plants play a crucial role in plant health, pest and disease defense, and fruit yield by actively participating in the plant's adaptation to its environment. In this study, high-throughput sequencing technology was employed to analyze the community structure and diversity of endophytic and rhizospheric soil microorganisms in Berchemia polyphylla var. leioclada. The results revealed significant differences in microbial diversity and community structure between the soil and plant compartments within the same geographic region. Microbial diversity and species composition varied among different geographic locations. The dominant bacteria in plants were Cyanobacteria and Proteobacteria, with dominant genera including Methylobacterium-Methylorubrum, Escherichia-Shigella and Sphingomonas. In contrast, the dominant bacteria in soil were Proteobacteria, Acidobacteriota, and Actinobacteriota, with dominant genera such as Sphingomonas, Conexibacter and Vicinamibacteraceae, with Sphingomonas was considered core groups present in all plant and soil samples. As for fungi, the dominant phyla in both plants and soil were Ascomycota, Basidiomycota, and Mortierellomycota, with different dominant genera between the two compartments, including Fusarium, Septoria, and Mortierella, totaling 59 genera. Linear discriminant analysis at the genus level identified 102 bacterial and 54 fungal indicator taxa associated with plants and soil. Co-occurrence network analysis indicated close interactions among soil bacterial microorganisms. Functional prediction of the top 10 microbial genes revealed three bacterial metabolic pathways shared between soil and plants, while the predominant fungal metabolic types were similar between the two compartments but with varying abundances. This study elucidates the diversity and interplay of endophytic and rhizospheric microorganisms in Berchemia polyphylla var. leioclada across diverse geographical regions, providing insights crucial for the plant's conservation and development.

Microbiome changes through the ontogeny of the marine sponge Crambe crambe

BackgroundPoriferans (sponges) are highly adaptable organisms that can thrive in diverse marine and freshwater environments due, in part, to their close associations with internal microbial communities. This sponge microbiome can be acquired from the surrounding environment (horizontal acquisition) or obtained from the parents during the reproductive process through a variety of mechanisms (vertical transfer), typically resulting in the presence of symbiotic microbes throughout all stages of sponge development. How and to what extent the different components of the microbiome are transferred to the developmental stages remain poorly understood. Here, we investigated the microbiome composition of a common, low-microbial-abundance, Atlantic-Mediterranean sponge, Crambe crambe, throughout its ontogeny, including adult individuals, brooded larvae, lecithotrophic free-swimming larvae, newly settled juveniles still lacking osculum, and juveniles with a functional osculum for filter feeding.ResultsUsing 16S rRNA gene analysis, we detected distinct microbiome compositions in each ontogenetic stage, with variations in composition, relative abundance, and diversity of microbial species. However, a particular dominant symbiont, Candidatus Beroebacter blanensis, previously described as the main symbiont of C. crambe, consistently occurred throughout all stages, an omnipresence that suggests vertical transmission from parents to offspring. This symbiont fluctuated in relative abundance across developmental stages, with pronounced prevalence in lecithotrophic stages. A major shift in microbial composition occurred as new settlers completed osculum formation and acquired filter-feeding capacity. Candidatus Beroebacter blanensis decreased significatively at this point. Microbial diversity peaked in filter-feeding stages, contrasting with the lower diversity of lecithotrophic stages. Furthermore, individual specific transmission patterns were detected, with greater microbial similarity between larvae and their respective parents compared to non-parental conspecifics.ConclusionsThese findings suggest a putative vertical transmission of the dominant symbiont, which could provide some metabolic advantage to non-filtering developmental stages of C. crambe. The increase in microbiome diversity with the onset of filter-feeding stages likely reflects enhanced interaction with environmental microbes, facilitating horizontal transmission. Conversely, lower microbiome diversity in lecithotrophic stages, prior to filter feeding, suggests incomplete symbiont transfer or potential symbiont digestion. This research provides novel information on the dynamics of the microbiome through sponge ontogeny, on the strategies for symbiont acquisition at each ontogenetic stage, and on the potential importance of symbionts during larval development.

Comparative Evaluation of Microbial Flora of Endodontic Origin in Teeth with Endo-Perio Lesions

ABSTRACT Background: Endodontic microbial flora plays a pivotal role in the development and persistence of periodontal endodontic lesions (PELs). Understanding the composition and prevalence of microbial species in PELs is essential for effective treatment strategies Materials and Methods: Microbial samples were collected from 50 teeth diagnosed with PELs. Sterile paper points were used to obtain samples from the root canals. Deoxyribonucleic acid (DNA) was extracted and subjected to polymerase chain reaction (PCR) amplification of the 16S ribosomal RNA (rRNA) gene to identify bacterial species. The obtained data were analyzed using statistical methods. Results: The microbial analysis revealed a diverse range of bacterial species in PELs. The most prevalent species were Porphyromonas gingivalis (32.5%), Treponema denticola (28.0%), and Fusobacterium nucleatum (22.5%). Streptococcus mutans (9.0%) and Actinomyces naeslundii (8.0%) were also frequently detected. Additionally, Prevotella intermedia (7.0%), Aggregatibacter actinomycetemcomitans (3.5%), and Enterococcus faecalis (2.5%) were present in lower frequencies Conclusion: The presence of a diverse microbial flora in teeth with PELs underscores the polymicrobial nature of these lesions. The predominance of periodontal pathogens such as Porphyromonas gingivalis, Treponema denticola, and Fusobacterium nucleatum suggests a strong association between periodontal and endodontic infections. A comprehensive understanding of the microbial profile in PELs is crucial for tailored therapeutic approaches targeting the specific pathogens involved.

Analysis of nasal flora composition in children with perennial allergic rhinitis

Objective:This paper focuses on the diversity of nasal microbiota in children with perennial allergic rhinitis and the differences in species composition, which may be used in the future as a biomarker for disease progression and treatment. Methods:A total of 65 subjects were enrolled, including 35 perennial AR patients（AR group） and a Control group（CG group） of 30 children without AR. Collect basic information and examination reports of nasal swabs. 16S-rDNA high-throughput sequencing technology was used to detect the microbial sequence in nasal swabs, and the composition and difference of microbial diversity in each group were analyzed by bioinformatics methods. Results:The Simpson and Shannon index of the alpha diversity in the AR group had a significantly increase compared to the CG group. Beta diversity was not different between the groups. Staphylococcus（Firmicutes） of the AR group were significantly higher than that of the CG group, but Moraxella is lower than that of the CG group. Conclusion:Nasal microbial diversity and species composition of children with allergic rhinitis differ from those of healthy children, and how the differential microorganisms interact with the host and participate in immune regulation and inflammatory response requires further study.

Microbial co-occurrences on catheters from long-term catheterized patients

Catheter-associated urinary tract infections (CAUTIs), a common cause of healthcare-associated infections, are caused by a diverse array of pathogens that are increasingly becoming antibiotic resistant. We analyze the microbial occurrences in catheter and urine samples from 55 human long-term catheterized patients collected over one year. Although most of these patients were prescribed antibiotics over several collection periods, their catheter samples remain colonized by one or more bacterial species. Examination of a total of 366 catheter and urine samples identify 13 positive and 13 negative genus co-occurrences over 12 collection periods, representing associations that occur more or less frequently than expected by chance. We find that for many patients, the microbial species composition between collection periods is similar. In a subset of patients, we find that the most frequently sampled bacteria, Escherichia coli and Enterococcus faecalis, co-localize on catheter samples. Further, co-culture of paired isolates recovered from the same patients reveals that E. coli significantly augments E. faecalis growth in an artificial urine medium, where E. faecalis monoculture grows poorly. These findings suggest novel strategies to collapse polymicrobial CAUTI in long-term catheterized patients by targeting mechanisms that promote positive co-associations.

Effects of Chlorella fusca-supplemented diet on intestinal microbiota and gene expression related to metabolism, stress, and immune response in Chelon labrosus

Microalgae are emerging as promising alternatives to traditional fishmeal and crop ingredients in aquaculture diets. In this study, we aimed to characterize the intestinal microbiota and evaluate the transcription of genes related to metabolism, stress, and the immune system in various tissues of thick-lipped grey mullet (Chelon labrosus) fed a diet containing 15 % of microalga Chlorella fusca against a microalgae-free control diet for 90 days. After this period, the fish were challenged with Aeromonas hydrophila and polyinosinic–polycytidylic acid (poly I:C) to assess their immune response during 72 h. Microbiota analysis revealed that dietary inclusion of microalgae did not produce significant differences in intestine diversity compared to the control group. The dominant genera differed between the groups, with Pseudomonas and Mycoplasma most abundant in the fish fed with C. fusca, and Brevinema, Cetobacterium, and Pseudomonas predominant in the control group. Gene expression analysis indicated significant changes in hif3α, mhcII, ferritin, and mx genes in different organs of fish fed the microalgae-supplemented diet. Gene expression in the head kidney showed variations after A. hydrophila or poly I:C challenges, and higher peak values were observed in poly I:C-injected fish. Furthermore, c3 mRNA levels were significantly up-regulated in the fish fed with C. fusca at 24 h following A. hydrophila challenge. In conclusion, the inclusion of C. fusca in the fish diet modifies the composition of microbial species in the intestine but does not seem to affect its functionality. Regarding the influence on gene expression, the microalgae-supplemented diet effectively modulates the transcription of stress and immune-related genes, which may potentially enhance the fish resistance to stress and infections.

Functional genomic analysis of nutrient cycling of plant-soil continuum in the mossy biocrust in the Tengger Desert

The microbiome and metabolic processes occurring in the soil of the moss crust-soil continuum contribute to drive biogeochemical cycles. In this study, soil chemical properties of soil which was attached to bryophyte (BRS) and soil which was dropped from bryophyte (BBS) were analyzed. Differences in microbial species composition, metabolic pathways and related genes of these two different soil types were also analyzed. The results showed that the total organic carbon (TOC), total nitrogen (TN) and ammonium nitrogen (NH4+-N) content of BRS were significantly higher than those of BBS. The dominant phylum in the soil microbiome of the moss crust-soil continuum was Actinobacteria. Genes and metabolic pathways related to the carbon, nitrogen, phosphorus, and sulfur cycle differed between BRS and BBS. The carbon sequestration capacity of BRS was higher than that of BBS. The relative abundance of napA, narH and narI genes involved in denitrification and dissimilatory nitrate reduction in the BRS microbiome was significantly higher than that in the BBS microbiome, while the relative abundance of nasA, NR and nirA genes involved in assimilatory nitrate reduction in the BRS soil microbiome was significantly lower than that in the BBS soil microbiome. The relative abundance of glpQ genes encoding glycerophosphodiester phosphodiesterase in the BRS microbiome was significantly higher than that in the BBS microbime, while the relative abundance of pstS, pstA, pstC, pstB genes responsible for phosphate-specific transport systems in the BRS microbiome was significantly lower than that in the BBS microbiome. The abundance of the assimilatory sulfate-reducing metabolic pathway in the BRS microbiome was significantly higher than that in the BBS microbiome, while the dissimilatory sulfate-reducing metabolic pathway in the BRS microbiome was significantly lower than that in the BBS microbiome. The study found that the microbiome in the soil which was attached to bryophyte plays a more important role in the accumulation of soil nutrients in the Tengger Desert through biodiversity and metabolic activity.

Evaluation of the fate of wastewater effluent organic matter in receiving water: Effect of sequential photochemical and biological processes

Effluent organic matter (EfOM) discharged from wastewater treatment plants (WWTPs) carry substantial risks to river ecosystems. The fate and role of EfOM in the receiving water is affected by its exposure to sunlight and microbial processes, but the extent of these processes remains unclear. In this study, three-phase sequence of irradiation and microbial incubation with EfOM were conducted to compare the behavior of EfOM with that of natural organic matter in receiving rivers (RNOM). The dissolved organic carbon (DOC) in EfOM was degraded by 23% after three sequential phases, while that in RNOM was degraded by 19%. In the first phase, the irradiation of EfOM stimulated microbial respiration and growth by producing easily metabolizable less aromatic lignin-type molecules, leading to a 21% increase in biodegradation. Conversely, the irradiation of RNOM removed biodegradable lignin-type molecules, causing a 50% decreased in biodegradation. The second and third irradiation phases of EfOM and RNOM produced biodegradable lignin-type molecules, making their molecular compositions increasingly similar. The acute toxicity of EfOM decreased by 55%, and differences in microbial species composition between EfOM and RNOM waters decreased by 82% after the three-phase sequence. These findings can improve understanding of the fate of EfOM discharged into receiving rivers.

Combined Dietary Administration of Chlorella fusca and Ethanol-Inactivated Vibrio proteolyticus Modulates Intestinal Microbiota and Gene Expression in Chelon labrosus

The use of functional feeds in aquaculture is currently increasing. This study aimed to assess the combined impact of dietary green microalgae Chlorella fusca and ethanol-inactivated Vibrio proteolyticus DCF12.2 (CVP diet) on thick-lipped grey mullet (Chelon labrosus) juvenile fish. The effects on intestinal microbiota and the transcription of genes related to metabolism, stress, and the immune system were investigated after 90 days of feeding. Additionally, the fish were challenged with Aeromonas hydrophila and polyinosinic–polycytidylic acid (poly I:C) to evaluate the immune response. Microbiota analysis revealed no significant differences in alpha and beta diversity between the anterior and posterior intestinal sections of fish fed the control (CT) and CVP diets. The dominant genera varied between the groups; Pseudomonas and Brevinema were most abundant in the CVP group, whereas Brevinema, Cetobacterium, and Pseudomonas were predominant in the CT group. However, microbial functionality remained unaltered. Gene expression analysis indicated notable changes in hif3α, mhcII, abcb1, mx, and tnfα genes in different fish organs on the CVP diet. In the head kidney, gene expression variations were observed following challenges with A. hydrophila or poly I:C, with higher peak values seen in fish injected with poly I:C. Moreover, c3 mRNA levels were significantly up-regulated in the CVP group 72 h post-A. hydrophila challenge. To conclude, incorporating C. fusca with V. proteolyticus in C. labrosus diet affected the microbial species composition in the intestine while preserving its functionality. In terms of gene expression, the combined diet effectively regulated the transcription of stress and immune-related genes, suggesting potential enhancement of fish resistance against stress and infections.

Effect of different rice transplanting patterns on microbial community in water, sediment, and Procambarus clarkii intestine in rice-crayfish system.

Although the microbial ecology of integrated rice-crayfish farming systems is receiving increasing attention with the expanding application area in China, the effects of rice transplanting patterns on the microbial community of water, sediment and Procambarus clarkii intestine in rice-crayfish system has yet to be determined. This study explored the microbial community present in water, sediment and intestine samples from three transplant patterns (rice crayfish with wide-narrow row transplanting, rice-crayfish with normal transplanting and pond-crayfish, abbreviated as RC-W, RC, and PC, respectively) using high-throughput sequencing. The results showed that the dominant microbial taxa from sediment, surrounding water, and intestine at phylum level were Proteobacteria, Chloroflexi, Cyanobacteria, Actinobacteria, Bacteroidetes. The patterns of rice transplanting had significant effects on microbial biodiversity and species composition in surrounding water. The OTUs community richness of water under RC group was significantly higher than that of PC group and RC-W group. The OTU relative abundance of top 10 operational taxonomic units had significantly different (p < 0.05) in the water samples from the three groups. The intestinal OTU community richness of Procambarus clarkii in the three groups was positively correlated with the community richness of water. The proximity between intestinal and water samples in PCA diagram indicated that their species composition was more similar. The results also showed that rice transplanting patterns can affect intestinal microbial biodiversity of Procambarus clarkii and the intestinal microbial biodiversity correlated with water bodies. Although the intestinal microbial diversity of crayfish in RC-W group was lower than that in RC group, the relative abundance of potential pathogenic bacteria, such as Vibrio, Aeromonas, in intestine of the crayfish in the RC-W group was significantly decreased under rice wide-narrow row transplanting model. Redundancy analysis revealed that environmental parameters, such as pH, DO, nitrate, which regulate the composition of microbial community structures. This study provides an understanding for microbial response to different rice transplanting pattern in rice-crayfish farming system.

Comparative Microbiome Analysis of Three Epidemiologically Important Tick Species in Latvia.

(1) Background: Amplicon-based 16S rRNA profiling is widely used to study whole communities of prokaryotes in many niches. Here, we comparatively examined the microbial composition of three tick species, Ixodes ricinus, Ixodes persulcatus and Dermacentor reticulatus, which were field-collected in Latvia. (2) Methods: Tick DNA samples were used for microbiome analysis targeting bacterial 16S rDNA using next-generation sequencing (NGS). (3) Results: The results showed significant differences in microbial species diversity and composition by tick species and life stage. A close similarity between microbiomes of I. ricinus and I. persulcatus ticks was observed, while the D. reticulatus microbiome composition appeared to be more distinct. Significant differences in alpha and beta microbial diversity were observed between Ixodes tick life stages and sexes, with lower taxa richness indexes obtained for female ticks. The Francisella genus was closely associated with D. reticulatus ticks, while endosymbionts Candidatus Midichlorii and Candidatus Lariskella were associated with I. ricinus and I. persulcatus females, respectively. In I. ricinus females, the endosymbiont load negatively correlated with the presence of the Rickettsia genus. (4) Conclusions: The results of this study revealed important associations between ticks and their microbial community and highlighted the microbiome features of three tick species in Latvia.

High conservation of the dental plaque microbiome across populations with differing subsistence strategies and levels of market integration.

Industrialization-including urbanization, participation in the global food chain and consumption of heavily processed foods-is thought to drive substantial shifts in the human microbiome. While diet strongly influences stool microbiome composition, the influence of diet on the oral microbiome is largely speculative. Multiple ecologically distinct surfaces in the mouth, each harbouring a unique microbial community, pose a challenge to assessing changes in the oral microbiome in the context of industrialization, as the results depend on the oral site under study. Here, we investigated whether microbial communities of dental plaque, the dense biofilm on non-shedding tooth surfaces, are distinctly different across populations with dissimilar subsistence strategies and degree of industrialized market integration. Using a metagenomic approach, we compared the dental plaque microbiomes of Baka foragers and Nzime subsistence agriculturalists in Cameroon (n = 46) with the dental plaque and calculus microbiomes of highly industrialized populations in North America and Europe (n = 38). We found that differences in microbial taxonomic composition between populations were minimal, with high conservation of abundant microbial taxa and no significant differences in microbial diversity related to dietary practices. Instead, we find that the major source of variation in dental plaque microbial species composition is related to tooth location and oxygen availability, which may be influenced by toothbrushing or other dental hygiene measures. Our results support that dental plaque, in contrast to the stool microbiome, maintains an inherent stability against ecological perturbations in the oral environment.

Soil Nutrients, Enzyme Activities, and Microbial Communities along a Chronosequence of Chinese Fir Plantations in Subtropical China.

Forests undergo a long-term development process from young to mature stages, yet the variations in soil nutrients, enzyme activities, microbial diversity, and community composition related to forest ages are still unclear. In this study, the characteristics of soil bacterial and fungal communities with their corresponding soil environmental factors in the young, middle, and mature stages (7, 15, and 25-year-old) of Chinese fir plantations (CFP) in the subtropical region of China were investigated in 2021. Results showed that the alpha diversity indices (Chao1 and Shannon) of soil bacteria and fungi were higher in 15 and 25-year-old stands than in 7-year-old stand of CFP, while the soil pH, soil water content, soil organic carbon, total nitrogen, total phosphorus, sucrase, urease, acid phosphatase, catalase, and microbial biomass carbon, nitrogen, and phosphorus showed higher in 7-year-old stand than other two stands of CFP. The nonmetric multidimensional scaling analysis revealed that the soil microbial species composition was significantly different in three stand ages of CFP. The redundancy and canonical correspondence analysis indicated that the soil urease and microbial biomass nitrogen were the main factors affecting soil bacterial and fungal species composition. Our findings suggested that soil microbial diversity and community structure were inconsistent with changes in soil nutrients and enzyme activities during CFP development, and enhancing stand nurturing and soil nutrient accumulation in the mid-development stage were beneficial to the sustainable management of CFP.

Fecal matters: Microbial signatures distinguish clinically relevant subtypes of precancerous colorectal polyps

Colorectal cancer (CRC) can arise from adenomatous or serrated polyps, which differ in their detection rate and risk of cancer progression. In this issue, Lee etal. report that these polyp subtypes demonstrate distinct fecal microbial species composition and metabolic potential that associate with diet and medications.