Abundance Of Bacterial Genera Research Articles

Stoichiometry regulates rice straw-induced priming effect: The microbial life strategies

Straw and nutrients retained in soil are crucial for priming effect (PE) and consequently for soil organic matter (SOM) turnover. However, the mechanisms by which carbon (C), nitrogen (N), and phosphorus (P) and their stoichiometric ratios impact microbial communities and regulate the PE intensity remain controversial, particularly in the flooded rice soils. In this work, the PE dynamics and microbial life strategies were measured over 100 days following an analysis of C:N:P stoichiometry after 13C labeled straw and nutrient inputs. P was the most limiting nutrient for microorganisms in Straw + N, and soil organic matter (SOM) decomposition was thus reduced by 18%. This was evidenced by: (i) the highest stoichiometric imbalance of C:P (0.97) between available resources and microbial biomass, (ii) the highest dissolved organic C (DOC):Olsen P ratio (140), and (iii) the lowest bacterial abundance. In contrast, lowering the soil C:P ratio (65) under straw + NP accelerated SOM decomposition. Compared to straw + N, the bacterial gene abundance increased by 170% under straw + NP, and the relative abundance of Y-strategists (Firmicutes, Betaproteobacteria, Gammaproteobacteria and Bacteroidetes) was 6.8 times greater than that of straw + N, suggesting that P was a major limiting factor for microbes in this paddy soil. With the depletion of available C during incubation, bacterial gene abundance decreased for 9 times, and the abundance of Firmicutes decreased from 39% to 19%, the abundance of Deltaproteobacteria increased from 20% to 24%, indicating a shift from Y-strategists to A-strategists and acquiring the resources from SOM and inducing positive PE. Our study elucidates the complex and dynamic linkages between C, N and P and their available ratio in resources, and evidence changes in the microbial community structure and PE.

O-268 Re-considering the endometrial microbiome: a comparison of DNA- and RNA-based sequencing techniques within the same cohort

Abstract Study question Does the analysis of the endometrial microbiome provide the same information when using DNA or RNA sequencing-based techniques? Summary answer DNA vs. RNA-based microbiome analysis techniques demonstrate significant microbial compositional differences, meaning that the previous endometrial 16S rRNA gene-based microbiome analysis results might be overestimated. What is known already In recent years, high-throughput sequencing technologies have revolutionised the field of reproductive microbiome research. Our understanding of the composition of endometrial microbiome predominantly relies on DNA-based 16S rRNA gene profiling method. Regardless of its effectiveness and low cost, its underestimation of microbial diversity, abundance, or functionality and lack of detection precision on species level have been highlighted. The meta-transcriptome analysis, RNA-based method, overcomes these limitations and identifies functional genes that are actively expressed by the alive microbes. This study aims to elucidate for the first time the endometrial microbiome using a dual approach of 16S rRNA gene-method and meta-transcriptomic analyses. Study design, size, duration In total forty-seven women with infertility at ages 27-42 years old were enrolled in the present study. Paired endometrial samples, endometrial brushing and Pipelle biopsy were collected from each participant at the mid-secretory menstrual phase (LH + 7/9). Participants/materials, setting, methods Endometrial samples were collected using Tao Brush for 16S rRNA analysis (DNA analysis) and Pipelle endometrial curette for meta-transcriptomic analysis (total RNA analysis). QIAamp UCP Pathogen Mini Kit was used for DNA extraction and 16S rRNA gene V3-V4 regions were sequenced on MiSeq. RNA was extracted using miRNeasy Micro kit, with rRNA removal by RiboZero kit and Libraries were generated using Stranded Total RNA Prep. Taxonomy was assigned by using Kraken2 (v2.2.1), Bracken (v2.7). Main results and the role of chance To the best of our knowledge, this is the first study to compare endometrial microbial identification using both metagenomics (16S rRNA sequencing) and meta-transcriptomics (meta-RNA sequencing) within the same cohort. Analysis of the composition of the microorganisms by bacterial 16S rRNA gene sequencing revealed that the most abundant bacterial genus in the endometrium was Lactobacillus. In the meta-transcriptome analysis, no microorganisms belonging to the Lactobacillus genus were detected in high abundance. This indicates that the relative abundance of this genus at the DNA level does not necessarily imply microbial activity or the presence of viable Lactobacillus in the endometrium. The meta-transcriptomics analysis detected microbial taxa such as Staphylococcus, Bacillus, Streptococcus, and Burkholderia as the most dominant. The results suggest that DNA-based detection of microorganisms in the endometrium may be overestimated due to the presence of naked DNA sequences or microorganisms from the vagina and cervix. Furthermore, RNA-based analysis demonstrates a population of active microorganisms different from the image shown by DNA analysis. Altogether, our study results indicate that the uterine microenvironment, as previously identified through DNA sequencing, may partly reflect the vaginocervical microenvironment, with the uterine tissue being a low biomass site not dominated by lactobacilli. Limitations, reasons for caution The endometrial samples were paired; however, DNA was analysed in the endometrial brushing sample while RNA in the tissue biopsy, which might result in some differences in microbial composition. Wider implications of the findings Contrary to the general belief of the Lactobacillus dominance in the human endometrium, our study suggests that the endometrial microenvironment may be harbouring DNA fragments and/or cells of lactobacilli originating from the lower reproductive tract. Our study results call out to re-consider/re-analyse the endometrial microbiome in health and disease. Trial registration number not applicable

The Influence of Increasing Roughage Content in the Diet on the Growth Performance and Intestinal Flora of Jinwu and Duroc × Landrace × Yorkshire Pigs.

The Jinwu pig (JW) is a hybrid breed originating from the Chinese indigenous Jinhua pig and Duroc pig, boasting excellent meat quality and fast growth rates. This study aimed to verify the tolerance of JW to roughage, similar to most Chinese indigenous pigs. In this research, two types of feed were provided to JW and Duroc × Landrace × Yorkshire pigs (DLY): a basal diet and a roughage diet (increasing the rice bran and wheat bran content in the basal diet from 23% to 40%) for a 65-day experimental period. The roughage diet showed an increasing trend in the feed conversion ratio (F/G), with a 17.61% increase in feed consumption per unit weight gain for DLY, while the increase for JW was only 4.26%. A 16S rRNA sequencing analysis revealed that the roughage diet increased the relative abundance of beneficial bacteria, such as Lactobacillus and Clostridium, while reducing the relative abundance of some potential pathogens, thus improving the gut microbiota environment. After being fed with the roughage diet, the abundance of bacterial genera, such as Treponema, Terrisporobacter, Coprococcus, and Ruminococcaceae, which aid in the digestion and utilization of dietary fiber, were significantly higher in Jinwu compared to DLY, indicating that these bacterial genera confer Jinwu with a higher tolerance to roughage than DLY.

Antibiotic treatment induces microbiome dysbiosis and reduction of neuroinflammation following traumatic brain injury in mice.

The gut microbiome is linked to brain pathology in cases of traumatic brain injury (TBI), yet the specific bacteria that are implicated are not well characterized. To address this gap, in this study, we induced traumatic brain injury (TBI) in male C57BL/6J mice using the controlled cortical impact (CCI) injury model. After 35 days, we administered a broad-spectrum antibiotics (ABX) cocktail (ampicillin, gentamicin, metronidazole, vancomycin) through oral gavage for 2 days to diminish existing microbiota. Subsequently, we inflicted a second TBI on the mice and analyzed the neuropathological outcomes five days later. Longitudinal analysis of the microbiome showed significant shifts in the diversity and abundance of bacterial genera during both acute and chronic inflammation. These changes were particularly dramatic following treatment with ABX and after the second TBI. ABX treatment did not affect the production of short-chain fatty acids (SCFA) but did alter intestinal morphology, characterized by reduced villus width and a lower count of goblet cells, suggesting potential negative impacts on intestinal integrity. Nevertheless, diminishing the intestinal microbiome reduced cortical damage, apoptotic cell density, and microglial/macrophage activation in the cortical and thalamic regions of the brain. Our findings suggest that eliminating colonized gut bacteria via broad-spectrum ABX reduces neuroinflammation and enhances neurological outcomes in TBI despite implications to gut health.

Profiling sediment bacterial communities and the response to pattern-driven variations of total nitrogen and phosphorus in long-term polyculture ponds

Sediment bacterial communities are decisive drivers of nutrient cycling processes in aquaculture ecosystems and are readily affected by surrounding environmental factors. However, the knowledge of sediment nutrient accumulations and bacterial community structure is limited in the emerging polyculture systems. Herein, we investigated the profiles of sediment properties and bacterial communities in six typical polyculture ponds and primarily explored the influence of total nitrogen and phosphorus on the bacterial species and diversity. In almost all sediment samples, Proteobacteria, Chloroflexi, and Bacteroides were the dominant species at the phylum level, and the five most abundant bacterial genera were Sulfurovum, Woeseia, Ilumatobacter, Robiginitalea, and Cyanobium_PCC-6307. A clear different bacterial community was observed with the most dominant bacterial phylum Firmicutes and the lowest bacterial diversity in TZ1 pond sediment; meanwhile, the TZ1 pond also showed the highest TN and TP concentrations. Notably, sediments from WZ1 and WZ2 ponds in low-latitude regions exhibited higher bacterial richness and diversity. Based on Pearson’s correlation analysis, bacterial α-diversity indices showed significant negative correlation with sediment TP content, and TN content contributed the most to the abundance of sediment dominant bacterial genus, indicating that the bacterial community is highly associated with sediment nutrient concentrations. Moreover, co-occurrence network analysis further revealed some keystone taxa that exhibited high correlations with other bacterial species, especially the high-abundance genus Robiginitalea bridging a large number of connections. Compared to traditional mono-mariculture pattern, our study provided direct evidence of lower nutrient loadings and different bacterial communities in the polyculture ponds. This could assist polyculture practitioners in developing effective strategies for detailed nutritional management.

Oral microbiome dysbiosis among cigarette smokers and smokeless tobacco users compared to non-users

Tobacco use significantly influences the oral microbiome. However, less is known about how different tobacco products specifically impact the oral microbiome over time. To address this knowledge gap, we characterized the oral microbiome of cigarette users, smokeless tobacco users, and non-users over 4 months (four time points). Buccal swab and saliva samples (n = 611) were collected from 85 participants. DNA was extracted from all samples and sequencing was carried out on an Illumina MiSeq, targeting the V3–V4 region of the 16S rRNA gene. Cigarette and smokeless tobacco users had more diverse oral bacterial communities, including a higher relative abundance of Firmicutes and a lower relative abundance of Proteobacteria, when compared to non-users. Non-users had a higher relative abundance of Actinomyces, Granulicatella, Haemophilus, Neisseria, Oribacterium, Prevotella, Pseudomonas, Rothia, and Veillonella in buccal swab samples, compared to tobacco users. While the most abundant bacterial genera were relatively constant over time, some species demonstrated significant shifts in relative abundance between the first and last time points. In addition, some opportunistic pathogens were detected among tobacco users including Neisseria subflava, Bulleidia moorei and Porphyromonas endodontalis. Overall, our results provide a more holistic understanding of the structure of oral bacterial communities in tobacco users compared to non-users.

Sphingomonas clade and functional distribution with simulated climate change.

Microbes are essential for the functioning of all ecosystems, and as global warming and anthropogenic pollution threaten ecosystems, it is critical to understand how microbes respond to these changes. We investigated the climate response of Sphingomonas, a widespread gram-negative bacterial genus, during an 18-month microbial community reciprocal transplant experiment across a Southern California climate gradient. We hypothesized that after 18 months, the transplanted Sphingomonas clade and functional composition would correspond with site conditions and reflect the Sphingomonas composition of native communities. We extracted Sphingomonas sequences from metagenomic data across the gradient and assessed their clade and functional composition. Representatives of at least 12 major Sphingomonas clades were found at varying relative abundances along the climate gradient, and transplanted Sphingomonas clade composition shifted after 18 months. Site had a significant effect (PERMANOVA; P < 0.001) on the distribution of both Sphingomonas functional (R2 = 0.465) and clade composition (R2 = 0.400), suggesting that Sphingomonas composition depends on climate parameters. Additionally, for both Sphingomonas clade and functional composition, ordinations revealed that the transplanted communities shifted closer to the native Sphingomonas composition of the grassland site compared with the site they were transplanted into. Overall, our results indicate that climate and substrate collectively determine Sphingomonas clade and functional composition.IMPORTANCESphingomonas is the most abundant gram-negative bacterial genus in litter-degrading microbial communities of desert, grassland, shrubland, and forest ecosystems in Southern California. We aimed to determine whether Sphingomonas responds to climate change in the same way as gram-positive bacteria and whole bacterial communities in these ecosystems. Within Sphingomonas, both clade composition and functional genes shifted in response to climate and litter chemistry, supporting the idea that bacteria respond similarly to climate at different scales of genetic variation. This understanding of how microbes respond to perturbation across scales may aid in future predictions of microbial responses to climate change.

Abstract 2178: Metagenomic analysis unveils the microbial landscape of pancreatic tumors

Abstract The composition of resident microbes in the human body is linked to various diseases and their treatment outcomes. Although studies have identified pancreatic ductal adenocarcinoma (PDAC) associated bacterial communities in the oral and gut samples, herein we hypothesize the prevalence of microbiota in pancreatic tumor tissues is different as compared to their matched adjacent, histologically normal appearing tissues and these microbial molecular signatures can be highly useful for PDAC diagnosis/prognosis. In this study, we performed comparative profiling of bacterial populations in pancreatic tumors and their respective adjacent normal tissues using 16S rRNA-based metagenomics analysis. This study revealed a higher abundance of Proteobacteria and Actinomycetota in tumor tissues compared to adjacent normal tissues. Interestingly, the Linear Discriminant Analysis (LDA) scores unambiguously revealed an enrichment of Delftia in tumor tissues, whereas Sphingomonas, Streptococcus, and Citrobacter exhibited depletion in tumor tissues. Furthermore, we analyzed the microbial composition between different groups of patients with different tumor differentiation stages. The bacterial genera, Delftia and Staphylococcus were very high in G1 stages (well differentiated) compared to G2 (well to moderate/moderately differentiated) and G3/G4 (poorly differentiated). However, the abundance of Actinobacter and Cloacibacterium was found to be very high in G2 and G3, respectively. Additionally, we evaluated the correlation of PD-L1 expression with the abundance of bacterial genera in tumor lesions. Our results indicated that three genus such as Streptomyces, Cutibacterium, and Delftia have a positive correlation with PD-L1 expression. Collectively, these findings demonstrate that PDAC lesions harbor relatively different microbiota compared to their normal tumor-adjacent tissues, and this information might be helpful for the diagnosis and prognosis of PADC patients. Citation Format: Sheema Khan, Goutam Banerjee, Saini Setua, Anupam Dhasmana, Pratik Banerjee, Murali Mohan Yallapu, Stephen W. Behrman, Subhash Chauhan, Daleniece Higgins Jones, Bhavin Chauhan. Metagenomic analysis unveils the microbial landscape of pancreatic tumors [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 2178.

Comparative analysis of the gut bacteria and fungi in migratory demoiselle cranes (Grus virgo) and common cranes (Grus grus) in the Yellow River Wetland, China.

Gut microbiota are closely related to the nutrition, immunity, and metabolism of the host and play important roles in maintaining the normal physiological activities of animals. Cranes are important protected avian species in China, and they are sensitive to changes in the ecological environment and are thus good environmental indicators. There have been no reports examining gut fungi or the correlation between bacteria and fungi in wild Demoiselle cranes (Grus virgo) and Common cranes (Grus grus). Related research can provide a foundation for the protection of rare wild animals. 16S rRNA and ITS high-throughput sequencing techniques were used to analyze the gut bacterial and fungal diversity of Common and Demoiselle cranes migrating to the Yellow River wetland in Inner Mongolia. The results revealed that for gut bacteria α diversity, Chao1 index in Demoiselle cranes was remarkably higher than that in Common cranes (411.07 ± 79.54 vs. 294.92 ± 22.38), while other index had no remarkably differences. There was no remarkable difference in fungal diversity. There were marked differences in the gut microbial composition between the two crane species. At the phylum level, the highest abundance of bacteria in the Common crane and Demoiselle crane samples was Firmicutes, accounting for 87.84% and 74.29%, respectively. The highest abundance of fungi in the guts of the Common and Demoiselle cranes was Ascomycota, accounting for 69.42% and 57.63%, respectively. At the genus level, the most abundant bacterial genus in the Common crane sample was Turicibacter (38.60%), and the most abundant bacterial genus in the Demoiselle crane sample was Catelicoccus (39.18%). The most abundant fungi in the Common crane sample was Penicillium (6.97%), and the most abundant fungi in the Demoiselle crane sample was Saccharomyces (8.59%). Correlation analysis indicated that there was a significant correlation between gut bacteria and fungi. This study provided a research basis for the protection of cranes. Indeed, a better understanding of the gut microbiota is very important for the conservation and management of wild birds, as it not only helps us to understand their life history and related mechanisms, but also can hinder the spread of pathogenic microorganisms.

A hitchhiker’s guide: estimates of microbial biomass and microbial gene abundance in soil

Information on microbial biomass carbon (MBC) is crucial to assess their stocks and role for plant nutrient release in soil. Next to fumigation-extraction, molecular methods are routinely used to estimate the contribution of fungi, bacteria, and archaea to the soil microbial community. However, more information on the links between these different indices would deepen the understanding of microbial processes. The current study is based on 11 datasets, which contain MBC and MBN data obtained by fumigation-extraction and information on bacterial, archaeal, and fungal gene abundance, totalling 765 data points from agricultural, forest, and rangeland soils. Some of these datasets additionally provide information on double-stranded deoxyribonucleic acid (dsDNA) and fungal ergosterol. MBC varied around the median of 206 µg g−1 soil. MBN followed with a median MB-C/N ratio of 4.1. Median microbial gene abundance declined from bacteria (96 × 108) to archaea (4.4 × 108) to fungi (1.8 × 108). The median ratio of MBC/dsDNA was 15.8 and that of bacteria/dsDNA was 5.8 × 108 µg−1. The relationships between MBC and dsDNA as well as between bacterial gene abundance and dsDNA were both negatively affected by soil pH and positively by clay content. The median ergosterol/MBC and fungi/ergosterol ratios were 0.20% and 4.7 (n × 108 µg−1), respectively. The relationship between fungal gene abundance and ergosterol was negatively affected by soil pH and clay content. Our study suggests that combining fumigation-extraction with molecular tools allows more precise insights on the physiological interactions of soil microorganisms with their surrounding environment.

Microbial diversity in camel milk from Xinjiang, China as revealed by metataxonomic analysis.

The quality of raw camel milk is affected by its bacterial composition and diversity. However, few studies have investigated the bacterial composition and diversity of raw camel milk. In this study, we obtained 20 samples of camel milk during spring and summer in Urumqi and Hami, Xinjiang, China. Single-molecule real-time sequencing technology was used to analyze the bacterial community composition. The results revealed that there were significant seasonal differences in the bacterial composition and diversity of camel milk. Overall, Epilithonimonas was the most abundant bacterial genus in our samples. Through the annotated genes inferred by PICRUSt2 were mapped against KEGG database. Non-parametric analysis of the bacterial community prediction function revealed a strong bacterial interdependence with metabolic pathways (81.83%). There were clear regional and seasonal differences in level 3 metabolic pathways such as fat, vitamins, and amino acids in camel milk. In addition, we identified lactic acid bacteria in camel milk with antibacterial and anti-tumor activities. Our findings revealed that camel milk from Xinjiang had serious risk of contamination by psychrophilic and pathogenic bacteria. Our research established a crucial theoretical foundation for ensuring the quality and safety of camel milk, thereby contributing significantly to the robust growth of China's camel milk industry.

Correlation between bacterial microbiome and Legionella species in water from public bath facilities by 16S rRNA gene amplicon sequencing.

Public bath facilities are major sources of sporadic cases and outbreaks of Legionella infections. Recently, 16S rRNA gene amplicon sequencing has been used to analyze bacterial characteristics in various water samples from both artificial and natural environments, with a particular focus on Legionella bacterial species. However, the relationship between the bacterial community and Legionella species in the water from public bath facilities remains unclear. In terms of hygiene management, it is important to reduce the growth of Legionella species by disinfecting the water in public bath facilities. Our findings contribute to the establishment of appropriate hygiene management practices and provide a basis for understanding the potential health effects of using bath and shower water available in public bath facilities.

Metagenome-assembled genome reveals species and functional composition of Jianghan chicken gut microbiota and isolation of Pediococcus acidilactic with probiotic properties

BackgroundChickens are one of the most widely farmed animals worldwide and play a crucial role in meat and egg production. Gut microbiota is essential for chickens’ health, disease, growth, and egg production. However, native chickens such as Jianghan chickens have better meat and egg production quality than centralized chickens, their intestinal microbial diversity is richer, and the potential gut microbial resources may bring health benefits to the host.ResultsThe bacterial species composition in the gut microbiota of Jianghan chickens is similar to that of other chicken breeds, with Phocaeicola and Bacteroides being the most abundant bacterial genera. The LEfSe analysis revealed significant differences in species composition and functional profiles between samples from Jingzhou and the other three groups. Functional annotation indicated that the gut microbiota of Jianghan chickens were dominated by metabolic genes, with the highest number of genes related to carbohydrate metabolism. Several antibiotic resistance genes (ARGs) were found, and the composition of ARGs was similar to that of factory-farmed chickens, suggesting that antibiotics were widely present in the gut microbiota of Jianghan chickens. The resistance genes of Jianghan chickens are mainly carried by microorganisms of the Bacteroidota and Bacillota phylum. In addition, more than 829 isolates were selected from the microbiota of Jianghan chickens. Following three rounds of acid and bile tolerance experiments performed on all the isolated strains, it was determined that six strains of Pediococcus acidilactici exhibited consistent tolerance. Further experiments confirmed that three of these strains (A4, B9, and C2) held substantial probiotic potential, with P. acidilactici B9 displaying the highest probiotic potential.ConclusionsThis study elucidates the composition of the intestinal microbiota and functional gene repertoire in Jianghan chickens. Despite the absence of antibiotic supplementation, the intestinal microbial community of Jianghan chickens still demonstrates a profile of antibiotic resistance genes similar to that of intensively reared chickens, suggesting resistance genes are prevalent in free-ranging poultry. Moreover, Jianghan and intensively reared chickens host major resistance genes differently, an aspect seldom explored between free-range and pastured chickens. Furthermore, among the 829 isolates, three strains of P. acidilatici exhibited strong probiotic potential. These findings provide insights into the unique gut microbiota of Jianghan chickens and highlight potential probiotic strains offering benefits to the host.C1P5UZATuvCf_fXF2a8dUFVideo

Bacterial Skin Dysbiosis in Darier Disease

Introduction: Darier disease is a rare inherited disease with dominant skin manifestations including keratotic papules and plaques on sebaceous and flexural areas. Secondary infection of skin lesions is common, and Staphylococcus aureus commonly colonizes these lesions. The aim of the study was to characterize the bacterial microbiome of cutaneous Darier lesions compared to normal-looking skin and disease severity. Methods: All patients with a history of Darier followed up at Emek Medical Center were invited to participate in the study. Patients that did not use antibiotics in the past month and signed informed consent had four skin sites sampled with swabs: scalp, chest, axilla, and palm. All samples were analyzed for bacterial microbiome using 16S rDNA sequencing. Results: Two hundred and eighty microbiome samples obtained from lesional and non-lesional skin of the scalp, chest, axilla, and palm of 42 Darier patients were included in the analysis. The most abundant bacterial genera across all skin sites were Propionibacterium, Corynebacterium, Paracoccus, Micrococcus, and Anaerococcus. Scalp and chest lesions featured a distinct microbiome configuration that was mainly driven by an overabundance of Staphylococci species. Patients with more severe disease exhibited microbiome alterations in the chest, axilla, and palm compared with patients with only mild disease, driven by Peptoniphilus and Moryella genera in scalp and palmar lesions, respectively. Conclusion: Staphylococci were significantly associated with Darier lesions and drove Darier-associated dysbiosis. Severity of the disease was associated with two other bacterial genera. Whether these associations also hold a causative role and may serve as a therapeutic target remains to be determined and requires further investigation.

Abundance and Diversity of Several Bacterial Genera in the Mariculture Environment

Although there have been some studies on pathogenic bacteria and their pathogenicity in animals, few studies have assessed the effects of aquaculture on the diversity of potentially pathogenic bacteria. This study used Illumina sequencing and quantitative PCR to explore the diversity of several bacterial genera containing pathogenic bacteria in the mariculture environment and the intestines of different cultured animals. These bacterial genera can be divided into two categories: The first category (14 genera) had high abundances and a low coefficient of variation among similar samples were significantly correlated with the total number of bacteria (r2 &gt; 0.7, p ≈ 0). The other category (7 genera) with low abundances and a high coefficient of variation had no significant relationship with bacterial abundance. These results indicated that these bacterial genera had different responses and adaptation mechanisms to the aquaculture environment. Principal component analysis (PCA) showed that a high abundance of genera was closely related to the pond environment. The abundance of these bacterial genera in the animals’ intestines was much higher than source water, especially for Mycoplasma, Pseudoalteromonas, Vibrio, and Enterococcus, suggesting the aquaculture promoted the high abundance of these bacteria. This study provides a theoretical basis for sediment-associated pathogens acting as a potential pathogen source in the aquaculture environment. This study provides a strategy for disease prevention and control according to the characteristics of potential pathogens in the cultural process.

Domestication caused taxonomical and functional shifts in the wheat rhizosphere microbiota, and weakened the natural bacterial biocontrol against fungal pathogens

Modern crops might have lost some of their functional traits, required for interacting with beneficial microbes, as a result of the genotypic/phenotypic modifications that occurred during domestication. Here, we studied the bacterial and fungal microbiota in the rhizosphere of two cultivated wheat species (Triticum aestivum and T. durum) and their respective ancestors (Aegilops tauschii and T. dicoccoides), in three experimental fields, by using metabarcoding of 16S rRNA genes and ITS2, coupled with co-occurrence network analysis. Moreover, the abundance of bacterial genes involved in N- and P-cycles was estimated by quantitative PCR, and urease, alkaline phosphatase and phosphomonoesterase activities were assessed by enzymatic tests. The relationships between microbiota and environmental metadata were tested by correlation analysis. The assemblage of core microbiota was affected by both site and plant species. No significant differences in the abundance of potential fungal pathogens between wild and cultivated wheat species were found; however, co-occurrence analysis showed more bacterial–fungal negative correlations in the wild species. Concerning functions, the nitrogen denitrification nirS gene was consistently more abundant in the rhizosphere of A. tauschii than T. aestivum. Urease activity was higher in the rhizosphere of each wild wheat species in at least two of the research locations. Several microbiota members, including potentially beneficial taxa such as Lysobacter and new taxa such as Blastocatellaceae, were found to be strongly correlated to rhizospheric soil metadata. Our results showed that a functional microbiome shift occurred as a result of wheat domestication. Notably, these changes also included the reduction of the natural biocontrol potential of rhizosphere-associated bacteria against pathogenic fungi, suggesting that domestication disrupted the equilibrium of plant-microbe relationships that had been established during million years of co-evolution.

Spatial Variations in the Nasal Microbiota of Staff Working in a Healthcare-Associated Research Core Facility

Objective: Workers in the healthcare sector are exposed to a multitude of bacterial genera. The location of their work contributes significantly to shaping personal microbiomes. In this study, we investigated the role of the workspace on the nasal bacteriome of staff working in a healthcare-associated research facility. Methods: The anterior nares of 10 staff working in different laboratories on the ground and first floor of the research facility were aseptically swabbed. Genomic DNA from each sample was used to amplify the V3 and V4 regions of the 16S rRNA gene. The amplified products were sequenced using the MiSeq sequencer (Illumina). Operational taxonomic units were filtered through MG-RAST v.3.6. Taxonomic profiling and visualizations were performed in MicrobiomeAnalyst v2.0. Results: The Wilcoxson Sum test at median abundances (p < 0.05) indicated that seven taxa (Micromonosporaceae, Micromonospora, Lactobacillaceae, Lactobacillus, Betaproteobacteria, Burkholderiales, Pectobacterium) were significantly diverse between ground-floor and first-floor workers. The analysis of similarity coefficient was 0.412 (p < 0.03) between the ground and the first-floor workers. Random forest analysis predicted 15 features that were significantly different (p < 0.05) in individuals working in different laboratories. Species richness and evenness also differed according to the placement of individuals in respective laboratories. Conclusion: These findings add to the knowledge that the healthcare support staff are at a speculated occupational risk. A slight shift in the abundances of bacterial genera and species might lead to unwanted consequences. Continual monitoring is thus warranted.

Metagenomic analysis unveils the microbial landscape of pancreatic tumors.

The composition of resident microbes in the human body is linked to various diseases and their treatment outcomes. Although studies have identified pancreatic ductal adenocarcinoma (PDAC)-associated bacterial communities in the oral and gut samples, herein, we hypothesize that the prevalence of microbiota in pancreatic tumor tissues is different as compared with their matched adjacent, histologically normal appearing tissues, and these microbial molecular signatures can be highly useful for PDAC diagnosis/prognosis. In this study, we performed comparative profiling of bacterial populations in pancreatic tumors and their respective adjacent normal tissues using 16S rRNA-based metagenomics analysis. This study revealed a higher abundance of Proteobacteria and Actinomycetota in tumor tissues compared with adjacent normal tissues. Interestingly, the linear discriminant analysis (LDA) scores unambiguously revealed an enrichment of Delftia in tumor tissues, whereas Sphingomonas, Streptococcus, and Citrobacter exhibited a depletion in tumor tissues. Furthermore, we analyzed the microbial composition between different groups of patients with different tumor differentiation stages. The bacterial genera, Delftia and Staphylococcus, were very high at the G1 stages (well differentiated) compared with G2 (well to moderate/moderately differentiated) and G3/G4 (poorly differentiated) stages. However, the abundance of Actinobacter and Cloacibacterium was found to be very high in G2 and G3, respectively. Additionally, we evaluated the correlation of programmed death-ligand (PDL1) expression with the abundance of bacterial genera in tumor lesions. Our results indicated that three genera such as Streptomyces, Cutibacterium, and Delftia have a positive correlation with PD-L1 expression. Collectively, these findings demonstrate that PDAC lesions harbor relatively different microbiota compared with their normal tumor adjacent tissues, and this information may be helpful for the diagnosis and prognosis of PADC patients.

Revealing microbial patterns in the rhizosphere of pecan trees asymptomatic and symptomatic for Texas root rot using a high-throughput sequencing approach

The rhizosphere harbors diverse microbial communities that play crucial roles in nutrient cycling and plant health. Understanding the composition and dynamics of these communities is essential for optimizing agricultural productivity and disease management. In this study, bacterial and fungal communities in the rhizosphere of pecan trees (Carya illinoinensis) asymptomatic and symptomatic for Texas root rot were characterized using high-throughput sequencing of the 16S rRNA gene and ITS region. The results indicated that Proteobacteria and Actinobacteria were the predominant bacterial phyla in both conditions. The predominant fungal phyla comprised Basidiomycota and Ascomycota in symptomatic conditions and Ascomycota and Mortierellomycota in asymptomatic ones. At the genus level, Streptomyces and Pseudomonas were the most abundant bacterial genera; among fungi, Scleroderma and Psathyrella were predominant in symptomatic samples and Mortierella in asymptomatic samples. α-diversity analysis showed significant differences in the fungal community. Specific bacterial and fungal biomarkers for asymptomatic and symptomatic conditions were identified, highlighting their importance in the pecan tree rhizosphere. A total of six bacterial and seven fungal taxa were detected in symptomatic samples, while four bacterial and 16 fungal taxa were detected in asymptomatic ones. These included genera known for their roles in soil health, such as Pseudomonas, Kaistobacter, Streptomyces, Psathyrella, Scleroderma, and Mortierella. Co-occurrence network analysis revealed higher complexity and interaction levels among microbial communities in asymptomatic samples, suggesting a healthier network supporting microbial communities. This study provides comprehensive and valuable insights into microbiome dynamics and microbial resources for future studies aimed at improving agricultural production through the study of rhizosphere microorganisms.

Species- and strain-level diversity of Corynebacteria isolated from human facial skin

BackgroundSequencing of the human skin microbiome revealed that Corynebacterium is an ubiquitous and abundant bacterial genus on human skin. Shotgun sequencing further highlighted the microbial “dark matter” of the skin microbiome, consisting of microorganisms, including corynebacterial species that were not cultivated and genome-sequenced so far. In this pilot project, facial human skin swabs of 13 persons were cultivated to selectively obtain corynebacteria. 54 isolates were collected and 15 of these were genome-sequenced and the pan-genome was determined. The strains were biochemically characterized and antibiotic susceptibility testing (AST) was performed.ResultsAmong the 15 sequenced strains, nine different corynebacterial species were found, including two so far undescribed species, tentatively named “Corynebacterium vikingii” and “Corynebacterium borealis”, for which closed genome sequences were obtained. Strain variability beyond the species level was determined in biochemical tests, such as the variable presence of urease activity and the capacity to ferment different sugars. The ability to grow under anaerobic conditions on solid agar was found to be species-specific. AST revealed resistances to clindamycin in seven strains. A Corynebacterium pseudokroppenstedtii strain showed additional resistance towards beta-lactam and fluoroquinolone antibiotics; a chromosomally located 17 kb gene cluster with five antibiotic resistance genes was found in the closed genome of this strain.ConclusionsTaken together, this pilot study identified an astonishing diversity of cutaneous corynebacterial species in a relatively small cohort and determined species- and strain-specific individualities regarding biochemical and resistance profiles. This further emphasizes the need for cultivation-based studies to be able to study these microorganisms in more detail, in particular regarding their host-interacting and, potentially, -beneficial and/or -detrimental properties.