Impact of microbial-based biopreparations on soil quality, plant health, and fruit chemistry in raspberry cultivation.

Application of microbial-based biopreparations as a pre-harvest strategy offers a method to obtain sustainable agricultural practices and could be an important approach for advancing food science, promoting sustainability, and meeting global food market demands. The impact of a bacterial-fungal biopreparation mixture on soil-plant-microbe interactions, fruit chemical composition and yield of 7 raspberry clones was investigated by examining the structural and functional profiles of microbial communities within leaves, fruits, and soil. Biopreparation addition caused the enhancement of the microbiological utilization of specific compounds, such as d-mannitol, relevant in plant-pathogen interactions and overall plant health. The biopreparation treatment positively affected the nitrogen availability in soil (9-160%). The analysis of plant stress marker enzymes combined with the evaluation of fruit quality and chemical properties highlight changes inducted by the pre-harvest biopreparation application. Chemical analyses highlight biopreparations' role in soil and fruit quality improvement, promoting sustainable agriculture. This effect was dependent on tested clones, showing increase of soluble solid content in fruits, concentration of polyphenols or the sensory quality of the fruits. The results of the next-generation sequencing indicated increase in the effective number of bacterial species after biopreparation treatment. The network analysis showed stimulating effect of biopreparation on microbial communities by enhancing microbial interactions (increasing the number of network edges up to 260%) of and affecting the proportions of mutual relationships between both bacteria and fungi. These findings show the potential of microbial-based biopreparation in enhancing raspberry production whilst promoting sustainable practices and maintaining environmental homeostasis and giving inshght in holistic understanding of microbial-based approaches for advancing food science monitoring.

Illumina MiSeq 16S rRNA Gene Library Preparation for Poultry Processing Microbiome Analyses.

The standardization of the microbiome sequencing of poultry rinsates is essential for generating comparable microbial composition data among poultry processing facilities if this technology is to be adopted by the industry. Samples must first be acquired, DNA must be extracted, and libraries must be constructed. In order to proceed to library sequencing, the samples should meet quality control standards. Finally, data must be analyzed using computer bioinformatics pipelines. This data can subsequently be incorporated into more advanced computer algorithms for risk assessment. Ultimately, *a uniform sequencing pipeline will enable both the government regulatory agencies and the poultry industry to identify potential weaknesses in food safety.This chapter presents the different steps for monitoring the population dynamics of the microbiome in poultry processing using 16S rDNA sequencing.

Association Between Healthy Eating Index-2020 and Oral Microbiome Among Postmenopausal Women.

BACKGROUND: Dietary intake has been suggested to be associated with the oral microbiome, but no study has examined the association between overall diet quality and the oral microbiome. OBJECTIVES: This study aimed to investigate the cross-sectional association between the Healthy Eating Index-2020 (HEI-2020) and the diversity and composition of the oral microbiome among participants in the Buffalo Osteoporosis and Periodontal Disease (OsteoPerio) Study. METHODS: In 1175 postmenopausal women (mean age: 67 ± 7.0 y), we estimated the HEI-2020 scores for each woman from a food frequency questionnaire administered from 1997 to 2000. Bacterial DNA was extracted from subgingival plaque samples and analyzed using 16S ribosomal RNA sequencing. The alpha-diversity (within-sample diversity) and ß-diversity (between-sample diversity) across HEI-2020 quartiles were examined using analysis of covariance and permutational multivariate analysis of variance, respectively. The associations between the HEI-2020 score and the relative abundance of microbial taxa were examined by linear regression models. The analyses were further conducted for individual components of the HEI-2020. RESULTS: No statistically significant associations were observed between the HEI-2020 scores and alpha- or beta-diversity. However, greater consumption of seafood, plant proteins, and total protein and lower consumption of added sugars were positively associated with alpha-diversity. After we applied a false detection rate (FDR) correction, higher HEI-2020 scores were significantly associated with decreased abundance of Lautropia, Streptococcus gordonii, Cardiobacterium valvarum, and Cardiobacterium hominis, and increased abundance of Selenomonas sp. oral taxon 133 and Selenomonas dianae (FDR-adjusted P values < 0.10). Additionally, 28 other taxa were identified as being associated with HEI-2020 components. CONCLUSIONS: Although the HEI-2020 was associated with the composition, but not the diversity, of the oral microbiome, individual HEI-2020 components were associated with both its diversity and composition. Specific dietary components may have more impact on the diversity and composition of oral microbiome than overall diet quality assessed by the HEI-2020.

Neonatal gut microbiota profile and the association with retinopathy of prematurity in preterm infants.

BACKGROUND: To explore the role of gut microbiota in preterm infants at high risk of developing retinopathy of prematurity (ROP). METHODS: Preterm infants with gestational age (GA) < 32 weeks and/or birth weight (BW) < 1500 g born between 2020 and 2021 were prospectively enrolled. Their faecal samples were collected and analysed at different postnatal ages of life using 16S rRNA gene sequencing on the Miseq platform. The main outcome measures were the microbial diversity, taxonomy, relative abundance, bacterial predicted functional analysis, and their associations with different ROP groups. Subgroup analyses were performed by matching their GA and BW across different ROP groups. RESULTS: A total of 268 stool samples were collected from 110 preterm infants, including 13 with type 1 ROP, 44 with type 2 or mild ROP, and 53 without ROP. Type 1 ROP showed no significant difference in microbial diversity up to 8 postnatal weeks (p = 0.057), while type 2 and no ROP groups displayed increased diversity (p = 0.0015 and p = 0.049, respectively). Bifidobacterium genera was notably less abundant in type 1 ROP group at first postnatal week (p = 0.022) and remained low in subsequent weeks. Predicted functional analysis revealed enriched pathways in membrane transport, carbohydrate metabolism, amino acid metabolism, and replication and repair. CONCLUSIONS: Reduced gut microbial diversity may be associated with ROP development in high-risk preterm infants. Further research is needed to comprehend how early-life Bifidobacterium reduction affects metabolism and how targeting microbiome may help for ROP prevention and management.

ZIP8 A391T Crohn's Disease-Linked Risk Variant Induces Colonic Metal Ion Dyshomeostasis, Microbiome Compositional Shifts, and Inflammation.

BACKGROUND: The pathogenesis of Crohn's disease involves genetic and environmental factors, with the gut microbiome playing a crucial role. The Crohn's disease-associated variant rs13107325 in the SLC39A8 gene results in an A391T substitution in the ZIP8 metal ion transporter and has previously been linked to alterations in the colonic microbiome in variant carriers. We hypothesized that the A391T substitution alters metal ion homeostasis in the colonic mucosal-luminal interface, thereby inducing dysbiosis which may promote intestinal inflammation. METHODS: To evaluate this hypothesis, we generated a SLC39A8 A393T mouse model (matching human A391T). We first examined trace element abundance in the colonic mucosal epithelium and lumen of homozygous A393T and wild-type (WT) mice to determine if the variant affected metal distribution. We also performed 16S rRNA gene sequencing on colon samples at 2 months, 3-4 months, and 12 months of age, and conducted histological scoring of colon tissue collected from 5-month and 10-month old mice. RESULTS: Consistent with an effect of the variant on ZIP8 function, homozygous A393T mice exhibited increased cobalt in the colonic mucosa, but reduced iron, zinc, manganese, cobalt, copper, and cadmium in the colonic lumen. 16S rRNA gene sequencing of colon samples revealed variant-linked effects on microbiome beta diversity in 2-month-, 3-4-month-, and 12-month-old mice. Histological scoring showed spontaneous intestinal inflammation in 10-month but not in 5-month-old mice. Lastly, predicted pathway analysis of the microbiome samples revealed differential enrichment of iron-, zinc-, and cobalt-dependent pathways in A393T mice compared to wild-type controls. CONCLUSION: These results suggest that the variant in SLC39A8 primarily restricts metal availability to the microbiota, resulting in compositions that can adapt to the environment and that A393T-linked dysbiosis occurs prior to the onset of inflammation. This study paves the way for future studies investigating risk variants as microbiome-disease modifiers.

Cervical cancer microbiome analysis: comparing HPV 16 and 18 with other HPV types.

Differences in the cervicovaginal microbiome may influence the persistence of HPV and therefore, the progression to cervical cancer. We aimed to analyze and compare the metatranscriptome of cervical cancers positive for HPV 16 and 18 with those positive for other HPV types to understand the microbiome's influence on oncogenicity. RNA sequencing data from a total of 222 invasive cervical cancer cases (HPV16/18 positive (n=42) and HPV "Other types" (n=180)) were subjected to taxonomy classification (Kraken 2) including bacteria, virus and fungi to the level of species. With a median depth of 288,080.5 reads per sample, up to 107 species (38 bacterial, 16 viral and 53 fungal) were identified. Diversity analyses revealed no significant differences in viral or fungal species between HPV16/18 and other HPV types. Bacterial alpha diversity was significantly higher in the "Other HPV types" group for the Observed index (p=0.0074) (but not for Shannon). Cumulative species curves revealed greater species diversity in the "Other HPV types" group compared to "HPV16/18 but no significant differences in species abundance were found between HPV groups. The study did not detect strong significant microbiome differences between HPV 16/18 and other HPV types in cervical cancers. Further research is necessary to explore potential factors influencing the oncogenicity of different HPV types and their interaction with the cervical microbiome.

Effects of transgenic modification on the bacterial communities in different niches of maize under glyphosate toxicity.

Transgenic glyphosate-resistant maize has emerged as a way to expand the use of glyphosate for weed control. Studying the microbiome in the tissues and rhizosphere soil of transgenic plants is vital for understanding the glyphosate-resistant mechanism and optimizing the transgenic design of crops. In our study, the expression of a mutant cp4epsps gene in transgenic maize, which confers tolerance to glyphosate, was performed using the maize variety Xianyu 335 as the genetically modified acceptor line. This transgenic modification did not affect the initial bacterial community in the leaf, stem, or root of maize, but promoted a differential bacterial community in the rhizosphere soil. Under glyphosate application, the abundance of beneficial bacteria involved in N fixation and P solubilization in plant tissues and the rhizosphere soil of glyphosate-resistance maize were higher than those in the glyphosate-sensitive maize. In contrast, the abundance of pathogens had the opposite trend, suggesting that the enhanced health of transgenic maize prevented microbiome deterioration under glyphosate. The re-inoculation of bacterial strains isolated from glyphosate-resistance maize into the leaf and rhizosphere soil of glyphosate-sensitive maize resulted in an enhanced photosynthetic capacity in response to glyphosate, demonstrating the vital role of specific bacteria for glyphosate resistance. Our study provides important evidence of how transgenic maize tolerance to herbicides affects the bacterial communities across the maize niches under glyphosate toxicity.

Impact of postsurgical vaginal microbiome on high-risk HPV infection and recurrence risk in patients with cervical cancer and intraepithelial neoplasia: A retrospective study.

Purpose: This study aimed to determine the effect of postsurgical vaginal microbiome (VM) on high-risk human papillomavirus (hrHPV) infection and the risk of disease recurrence in patients surgically treated for cervical cancer (CC) or intraepithelial neoplasia (CIN). Methods: 207 women who underwent surgical treatment for CC or CIN at the Department of Gynecologic Oncology of the First Affiliated Hospital of University of Science and Technology of China from November 2016 to October 2023 were included. The patients' clinical data, including age, surgical modality, and diagnosis at time of index surgery, were collected retrospectively and analyzed. Associations between postsurgical VM indices, hrHPV infection, cervical cytology, and recurrence were also evaluated. Results: Patient age, surgical modality (whether complete excision of the cervix was performed), and diagnosis at time of index surgery (cervical dysplasia vs. cervical carcinoma) showed no significant association with postsurgical hrHPV infection, cervical cytology, or disease recurrence. However, postsurgical VM imbalance was significantly associated with hrHPV infection status (OR = 4.640, 95 % CI = 2.085-10.460, P < 0.001), abnormal cervical cytology (OR = 3.994, 95 % CI = 1.154-13.826, P = 0.020), and disease recurrence (OR = 3.789, 95 % CI = 1.091-13.154, P = 0.026). Among the specific VM indices, a vaginal pH above 4.5 (OR = 4.570, 95 % CI = 1.640-12.690, P = 0.002), a lactobacilli proportion below 50 % (OR = 3.938, 95 % CI = 1.299-11.934, P = 0.010), and the presence of aerobic vaginitis (AV, OR = 2.425, 95 % CI = 0.996-5.901, P = 0.046) were risk factors for postsurgical recurrence. Conclusion: Postsurgical VM imbalance, especially abnormal indices, such as a pH above 4.5, a lactobacilli proportion below 50 %, and the presence of AV, was associated with an increased risk of postsurgical recurrence in patients who underwent surgical treatment for CIN and CC. Monitoring and potentially intervening in the VM may improve the prognosis of these patients.

Microbial biomarkers as indicators of sperm viability in an insect.

Our understanding of microbial variation in male reproductive tissues is poorly understood, both regarding how it varies spatially across different tissues and its ability to affect male sperm and semen quality. To redress this gap, we explored the relationship between male sperm viability and male gut and reproductive tract microbiomes in the Pacific field cricket, Teleogryllus oceanicus. We selected cohorts of males within our populations with the highest and lowest natural sperm viability and characterized the bacterial microbiota present in the gut, testes, seminal vesicle, accessory glands and the spermatophore (ejaculate) using 16S ribosomal RNA gene metabarcoding. We identified bacterial taxa corresponding to sperm viability, highlighting for the first time an association between the host's microbial communities and male competitive fertilization success. We also found significant spatial variation in bacterial community structure of reproductive tissue types. Our data demonstrate the importance of considering the microbial diversity of both the host gut and reproductive tract when investigating male fertility in wildlife and potentially human clinical settings.

Chlorpyrifos modulates the mouse gut microbiota and metabolic activity.

The organophosphate chlorpyrifos is a commonly used pesticide for fruits and vegetables despite its association with neurotoxicity in humans. While some studies suggest that organophosphates may impact the gut microbiota, no studies to date have investigated the direct effect of chlorpyrifos on the gut microbiota with doses that approximate environmentally relevant dietary concentrations (EPA chronic reference dose: 0.3 µg/kg/day in humans and EPA acute reference dose: 5 µg/kg/day in humans). Thus, we examined the influence of chlorpyrifos on the gut microbiota by assessment of bacterial physiology and metabolism using flow cytometry, 1H NMR-based metabolomics, and changes in the cecal microbiota community with 16S rRNA amplicon sequencing and analysis. Chlorpyrifos did not directly damage bacteria but rather perturbed bacterial metabolism. Chlorpyrifos exposure to bacteria increased the concentration of amino acids, carbohydrates, and nucleic acids. The relative abundances of Lactobacillus, Allobaculum, Roseburia, and Butyricicoccus increased after exposure to chlorpyrifos. Analyses of the 16S rRNA gene amplicon data predicted decreased amino acid biosynthesis and nucleic acid degradation and increased glycolysis which was supported by 1H NMR-based metabolomics. Collectively, these results demonstrate that environmentally relevant doses of chlorpyrifos can impact the metabolic activity of isolated gut microbes which may result in an imbalance in overall gut metabolic activity.

Erratum: The growth-promoting and disease-suppressing mechanisms of Trichoderma inoculation on peanut seedlings.

[This corrects the article DOI: 10.3389/fpls.2024.1414193.].

Abiotic factors shape mosquito microbiomes that enhance host development.

Metazoans rely on interactions with microorganisms through multiple life stages. For example, developmental trajectories of mosquitoes can vary depending on the microorganisms available during their aquatic larval phase. However, the role that the local environment plays in shaping such host-microbe dynamics and the consequences for the host organism remain inadequately understood. Here, we examine the influence of abiotic factors, locally available bacteria, and their interactions on the development and associated microbiota of the mosquito Aedes albopictus. Our findings reveal that leaf detritus infused into the larval habitat water, sourced from native Hawaiian tree "ohi'a lehua Metrosideros polymorpha, invasive strawberry guava Psidium cattleyanum, or a pure water control, displayed a more substantial influence than either temperature variations or simulated microbial dispersal regimes on bacterial community composition in adult mosquitoes. However, specific bacteria exhibited divergent patterns within mosquitoes across detrital infusions which did not align with their abundance in the larval habitat. Specifically, we observed a higher relative abundance of a Chryseobacterium sp. strain in mosquitoes from the strawberry guava infusion than the pure water control, whereas the opposite trend was observed for a Pseudomonas sp. strain. In a follow-up experiment, we manipulated the presence of these two bacterial strains and found larval developmental success was enhanced by including the Chryseobacterium sp. strain in the strawberry guava infusion and the Pseudomonas sp. strain in the pure water control. Collectively, these data suggest that interactions between abiotic factors and microbes of the larval environment can help shape mosquito populations" success.

Genome sequencing of Enterococcus faecalis strain 13, an oral strain isolated from C57BL/6 mice.

Enterococcus faecalis strain 13 (Ef#13) is a tongue isolate from a C57BL/6 mouse with experimental oropharyngeal candidiasis. Short-read sequencing revealed a genome of 2,767,598 bp with a GC content of 38.4%, and 2,649 genes were predicted.

Contribution of the Gut Microbiome to the Perpetuation of Inflammation in Crohn's Disease: A Systematic Review.

Crohn's disease (CD) is a sub-type of inflammatory bowel disease (IBD) with a characteristic relapsing and remitting inflammation involving the gastrointestinal (GI) tract. Although there are several medications to relieve the symptoms, there is no definite cure for the condition. This paper highlights how CD affects our gut flora, which subsequently leads to the perpetuation of inflammation. This review was conducted according to Preferred Reporting Items for Systematic Review and Meta-Analysis (PRISMA) 2020 guidelines using PubMed, ScienceDirect, Multidisciplinary Digital Publishing Institute (MDPI), and Google Scholar as sources for relevant literature. After applying the quality appraisal tools, we finalized 11 articles for the paper. Inflammation seen in CD leads to dysbiosis, where there is a reduction in beneficial microbes such as Faecalibacterium and Roseburia species and an increase in pathogenic microbes such as Escherichia and Proteus species. This difference in gut microbes disrupts barrier function and immune processes in the intestine, contributing to the worsening of inflammation seen in CD. Several studies have been carried out to understand this complex relationship between the gut microbiome (GM) and CD, as it may serve as a potential novel therapeutic alternative, necessary as CD's burden is increasing globally.

Soil and root microbiome analysis and isolation of plant growth-promoting bacteria from hybrid buffaloberry (Shepherdia utahensis 'Torrey') across three locations.

The effects of climate change are becoming increasingly hazardous for our ecosystem. Climate resilient landscaping, which promotes the use of native plants, has the potential to simultaneously decrease the rate of climate change, enhance climate resilience, and combat biodiversity losses. Native plants and their associated microbiome form a holo-organism; interaction between plants and microbes is responsible for plants' growth and proper functioning. In this study, we were interested in exploring the soil and root microbiome composition associated with Shepherdia utahensis, a drought hardy plant proposed for low water use landscaping, which is the hybrid between two native hardy shrubs of Utah, S. rotudifolia and S. argentea. The bulk soil, rhizosphere, root, and nodule samples of the hybrid Shepherdia plants were collected from three locations in Utah: the Logan Campus, the Greenville farm, and the Kaysville farm. The microbial diversity analysis was conducted, and plant growth-promoting bacteria were isolated and characterized from the rhizosphere. The results suggest no difference in alpha diversity between the locations; however, the beta diversity analysis suggests the bacterial community composition of bulk soil and nodule samples are different between the locations. The taxonomic classification suggests Proteobacteria and Actinobacteriota are the dominant species in bulk soil and rhizosphere, and Actinobacteriota is solely found in root and nodule samples. However, the composition of the bacterial community was different among the locations. There was a great diversity in the genus composition in bulk soil and rhizosphere samples among the locations; however, Frankia was the dominant genus in root and nodule samples. Fifty-nine different bacteria were isolated from the rhizosphere and tested for seven plant growth-promoting (PGP) traits, such as the ability to fix nitrogen, phosphates solubilization, protease activity, siderophore, Indole Acetic Acid (IAA) and catalase production, and ability to use ACC as nitrogen source. All the isolates produced some amount of IAA. Thirty-one showed at least four PGP traits and belonged to Stenotrophomonas, Chryseobacterium, Massilia, Variovorax, and Pseudomonas. We shortlisted 10 isolates that showed all seven PGP traits and will be tested for plant growth promotion.

Molecular cross-talk among human intestinal bifidobacteria as explored by a human gut model.

Bifidobacteria are well known as common and abundant colonizers of the human gut and are able to exert multiple beneficial effects on their host, although the cooperative and competitive relationships that may occur among bifidobacterial strains are still poorly investigated. Therefore, to dissect possible molecular interactions among bifidobacterial species that typically colonize the human gut, three previously identified bifidobacterial prototypes, i.e., B. bifidum PRL2010, B. breve PRL2012, and B. longum PRL2022 were cultivated individually as well as in bi- and tri-association in a human gut-simulating medium. Transcriptomic analyses of these co-associations revealed up-regulation of genes predicted to be involved in the production of extracellular structures including pili (i.e., flp pilus assembly TadE protein gene), exopolysaccharides (i.e., GtrA family protein gene) and teichoic acids (i.e., ABC transporter permease), along with carbohydrate, amino acid and vitamin metabolism-related genes (i.e., exo-alpha-sialidase; beta-galactosidase and pyridoxamine kinase), suggesting that co-cultivation of bifidobacteria induces a response, in individual bifidobacterial strains, aimed at enhancing their proliferation and survival, as well as their ability to cooperate with their host to promote their persistence. Furthermore, exposure of the selected prototypes to human cell line monolayers unveiled the ability of the bifidobacterial tri-association to communicate with their host by increasing the expression of genes involved in adherence to/interaction with intestinal human cells. Lastly, bifidobacterial tri-association promoted the transcriptional upregulation of genes responsible for maintaining the integrity and homeostasis of the intestinal epithelial barrier.

Pulmonary fibrosis: pathogenesis and therapeutic strategies.

Pulmonary fibrosis (PF) is a chronic and progressive lung disease characterized by extensive alterations of cellular fate and function and excessive accumulation of extracellular matrix, leading to lung tissue scarring and impaired respiratory function. Although our understanding of its pathogenesis has increased, effective treatments remain scarce, and fibrotic progression is a major cause of mortality. Recent research has identified various etiological factors, including genetic predispositions, environmental exposures, and lifestyle factors, which contribute to the onset and progression of PF. Nonetheless, the precise mechanisms by which these factors interact to drive fibrosis are not yet fully elucidated. This review thoroughly examines the diverse etiological factors, cellular and molecular mechanisms, and key signaling pathways involved in PF, such as TGF-ß, WNT/ß-catenin, and PI3K/Akt/mTOR. It also discusses current therapeutic strategies, including antifibrotic agents like pirfenidone and nintedanib, and explores emerging treatments targeting fibrosis and cellular senescence. Emphasizing the need for omni-target approaches to overcome the limitations of current therapies, this review integrates recent findings to enhance our understanding of PF and contribute to the development of more effective prevention and management strategies, ultimately improving patient outcomes.

Intestinal microbial profiles of wild Alaskan rainbow trout (Oncorhynchus mykiss) characterized by 16S rRNA amplicon data.

Rainbow trout (Oncorhynchus mykiss) is a dominant aquaculture species of the Salmonidae family, native only to the North Pacific. Recently, the gut microbiome has been shown to reflect the health status and responses to environmental changes in farmed fish. In this analysis we investigated the microbiome composition of the intestinal tract in 20 wild-caught rainbow trout specimens sampled in Alaska, USA. The targeted 16S rRNA gene (V3-V4 region) was sequenced on the Illumina NovaSeq 6000 platform. After quality control, demultiplexing and adapter trimming reads were analyzed using the DADA2 pipeline to obtain Amplicon Sequencing Variants (ASVs) which were subsequently taxonomically assigned. We found two phyla dominating the gut ecosystem present in every sample, Firmicutes and Fusobacteria, followed by lower abundances of Cyanobacteria, Proteobacteria and Bacteroidetes. At the genus level, we found high relative abundances of Cetobacterium and Clostridium sensu stricto 1. Interestingly, we did not identify often dominant genera Mycoplasma, Pseudomonas or Weisella which were prevalent in numerous studies previously, in cultured rainbow trout. Wild fish are exposed to a plethora of unpredictable environmental challenges, ranging from fluctuating water temperatures to variable food availability, as opposed to controlled conditions in production facilities. Examining and comparing the gut ecosystem of wild and reared individuals holds great potential in optimizing management practices for commercially important species. Microbiome studies can provide novel ways to enhance the overall welfare of fish, strengthen disease prevention and increase sustainability in aquaculture production.