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Bibliography on: Microbiome

The Electronic Scholarly Publishing Project: Providing world-wide, free access to classic scientific papers and other scholarly materials, since 1993.


ESP: PubMed Auto Bibliography 22 Feb 2024 at 01:53 Created: 


It has long been known that every multicellular organism coexists with large prokaryotic ecosystems — microbiomes — that completely cover its surfaces, external and internal. Recent studies have shown that these associated microbiomes are not mere contamination, but instead have profound effects upon the function and fitness of the multicellular organism. We now know that all MCEs are actually functional composites, holobionts, composed of more prokaryotic cells than eukaryotic cells and expressing more prokaryotic genes than eukaryotic genes. A full understanding of the biology of "individual" eukaryotes will now depend on an understanding of their associated microbiomes.

Created with PubMed® Query: microbiome[tiab] NOT pmcbook NOT ispreviousversion

Citations The Papers (from PubMed®)


RevDate: 2024-02-21
CmpDate: 2024-02-21

Kitamura N, Kajihara T, Volpiano CG, et al (2024)

Exploring the effects of antimicrobial treatment on the gut and oral microbiomes and resistomes from elderly long-term care facility residents via shotgun DNA sequencing.

Microbial genomics, 10(2):.

Monitoring antibiotic-resistant bacteria (ARB) and understanding the effects of antimicrobial drugs on the human microbiome and resistome are crucial for public health. However, no study has investigated the association between antimicrobial treatment and the microbiome-resistome relationship in long-term care facilities, where residents act as reservoirs of ARB but are not included in the national surveillance for ARB. We conducted shotgun metagenome sequencing of oral and stool samples from long-term care facility residents and explored the effects of antimicrobial treatment on the human microbiome and resistome using two types of comparisons: cross-sectional comparisons based on antimicrobial treatment history in the past 6 months and within-subject comparisons between stool samples before, during and 2-4 weeks after treatment using a single antimicrobial drug. Cross-sectional analysis revealed two characteristics in the group with a history of antimicrobial treatment: the archaeon Methanobrevibacter was the only taxon that significantly increased in abundance, and the total abundance of antimicrobial resistance genes (ARGs) was also significantly higher. Within-subject comparisons showed that taxonomic diversity did not decrease during treatment, suggesting that the effect of the prescription of a single antimicrobial drug in usual clinical treatment on the gut microbiota is likely to be smaller than previously thought, even among very elderly people. Additional analysis of the detection limit of ARGs revealed that they could not be detected when contig coverage was <2.0. This study is the first to report the effects of usual antimicrobial treatments on the microbiome and resistome of long-term care facility residents.

RevDate: 2024-02-20

Wei C, Xu T, Geng Y, et al (2024)

High-fat diet disrupts the gut microbiome, leading to inflammation, damage to tight junctions, and apoptosis and necrosis in Nyctereutes procyonoides intestines.

Microbiology spectrum [Epub ahead of print].

Given the burgeoning Nyctereutes procyonoides breeding industry and its growing scale, it is imperative to investigate the impact of high-fat diets on the health of these animals. This study involved 30 male Nyctereutes procyonoides of comparable weights (3 kg ±0.5), randomly assigned to either a control group or a high-fat diet group (n = 15 each). The latter group was fed a mixture of lard and basal diet in a 2:5 ratio, establishing a high-fat diet model in Nyctereutes procyonoides. This diet induced diarrhea and histopathological changes in the Nyctereutes procyonoides. Analysis of the small intestine contents using 16S rRNA sequencing revealed a high-fat diet-induced disruption in the gut microbiota. Specifically, Escherichia-Shigella emerged as the biomarker in the high-fat diet group (P = 0.049), while Vagococcus was prevalent in the control group (P = 0.049), indicating a significant increase in harmful bacteria in the high-fat diet group. Furthermore, this disrupted gut flora correlated with inflammation and oxidative stress, as evidenced by marked increases in TNF-α (P < 0.01), IL-1β (P < 0.05), and IL-6 (P < 0.05) levels, measured via q-PCR, Western blot, and oxidative stress assays. In addition, q-PCR analysis revealed significant upregulation of apoptosis and necrosis markers, including Bax, Caspase3, Caspase9, Caspase12, RIPK3, and RIPK1 (P < 0.01 to P < 0.001), and a concurrent downregulation of the anti-apoptotic gene Bcl-2 (P < 0.01) in the high-fat diet group, consistent with protein expression trends. These findings suggest that a high-fat diet alters the gut microbiome toward a more harmful bacterial composition, escalating inflammatory responses and intestinal tissue permeability, culminating in intestinal cell apoptosis and necrosis.IMPORTANCEThis study examines the impact of high-fat diets on Nyctereutes procyonoides. Our research established a Nyctereutes procyonoides model on a high-fat diet, revealing significant health impacts, such as diarrhea, histological anomalies, and alterations in the gut microbiota. These findings emphasize the importance of preventing health issues and promoting sustainable industry growth. They highlight the significant impact of diet on gut microbiota and overall animal health.

RevDate: 2024-02-20

Yang J, Ding D, Zhang X, et al (2024)

A comparative analysis of soil physicochemical properties and microbial community structure among four shelterbelt species in the northeast China plain.

Microbiology spectrum [Epub ahead of print].

Conducting studies that focus on the alterations occurring in the soil microbiome within protection forests in the northeast plain is of utmost importance in evaluating the ecological rehabilitation of agricultural lands in the Mollisols region. Nevertheless, the presence of geographic factors contributes to substantial disparities in the microbiomes, and thus, addressing this aspect of influence becomes pivotal in ensuring the credibility of the collected data. Consequently, the objective is to compare the variations in soil physicochemical properties and microbial community structure within the understory of diverse shelterbelt species. In this study, we analyzed the understory soils of Juglans mandshurica (Jm), Fraxinus mandschurica (Fm), Acer mono (Am), and Betula platyphylla (Bp) from the same locality. We employed high-throughput sequencing technology and soil physicochemical data to investigate the impact of these different tree species on soil microbial communities, chemical properties, and enzyme activities in Mollisols areas. Significant variations in soil nutrients and enzyme activities were observed among tree species, with soil organic matter content ranging from 49.1 to 67.7 g/kg and cellulase content ranging from 5.3 to 524.0 μg/d/g. The impact of tree species on microbial diversities was found to be more pronounced in the bacterial community (Adnoism: R = 0.605) compared to the fungal community (Adnoism: R = 0.433). The linear discriminant analysis effect size (LEfSe) analysis revealed a total of 5 (Jm), 3 (Bp), and 6 (Am) bacterial biomarkers, as well as 2 (Jm), 6 (Fm), 4 (Bp), and 1 (Am) fungal biomarker at the genus level (LDA3). The presence of various tree species was observed to significantly alter the relative abundance of specific microbial community structures, specifically in Gammaproteobacteria, Ascomycota, and Basidiomycota. Furthermore, environmental factors, such as pH, total potassium, and available phosphorus were important factors influencing changes in bacterial communities. We propose that Fm be utilized as the primary tree species for establishing farmland protection forests in the northeastern region, owing to its superior impact on enhancing soil quality.IMPORTANCEThe focal point of this study lies in the implementation of a controlled experiment conducted under field conditions. In this experiment, we deliberately selected four shelterbelts within the same field, characterized by identical planting density, and planting year. This deliberate selection effectively mitigated the potential impact of extraneous factors on the three microbiomes, thereby enhancing the reliability and validity of our findings.

RevDate: 2024-02-20

Simbassa SB, Clark J, Salazar K, et al (2024)

Draft genome sequences of Pseudomonas strains zfem001-005 isolated from the intestine of larval zebrafish Danio rerio.

Microbiology resource announcements [Epub ahead of print].

Here, we report the draft genome sequences of Pseudomonas strains zfem001-005, five isolates from the intestinal microbiota of healthy larval zebrafish Danio rerio at a developmental age of 7 days post fertilization. The isolates have been identified as Pseudomonas sediminis, Pseudomonas japonica, Pseudomonas otitidis, Pseudomonas sichuanensis, and Pseudomonas tohonis, respectively.

RevDate: 2024-02-20

Huang J, Wu Y, Gao Q, et al (2024)

Metagenomic exploration of the rhizosphere soil microbial community and their significance in facilitating the development of wild-simulated ginseng.

Applied and environmental microbiology [Epub ahead of print].

Panax ginseng, a prized medicinal herb, has faced increasingly challenging field production due to soil degradation and fungal diseases in Northeast China. Wild-simulated cultivation has prevailed because of its sustainable soil management and low disease incidence. Despite the recognized benefits of rhizosphere microorganisms in ginseng cultivation, their genomic and functional diversity remain largely unexplored. In this work, we utilized shotgun metagenomic analysis to reveal that Pseudomonadota, Actinomycetota, and Acidobacteriota were dominant in the ginseng rhizobiome and recovered 14 reliable metagenome-assembled genomes. Functional analysis indicated an enrichment of denitrification-associated genes, potentially contributing to the observed decline in soil fertility, while genes associated with aromatic carbon degradation may be linked to allelochemical degradation. Further analysis demonstrated enrichment of Actinomycetota in 9-year-old wild-simulated ginseng (WSG), suggesting the need for targeted isolation of Actinomycetota bacteria. Among these, at least three different actinomycete strains were found to play a crucial role in fungal disease resistance, with Streptomyces spp. WY144 standing out for its production of actinomycin natural products active against the pathogenic fungus Ilyonectria robusta. These findings not only enhance our understanding of the rhizobiome of WSG but also present promising avenues for combating detrimental fungal pathogens, underscoring the importance of ginseng in both medicinal and agricultural contexts.IMPORTANCEWild-simulated ginseng, growing naturally without human interference, is influenced by its soil microbiome. Using shotgun metagenomics, we analyzed the rhizospheric soil microbiome of 7- and 9-year-old wild-simulated ginseng. The study aimed to reveal its composition and functions, exploring the microbiome's key roles in ginseng growth. Enrichment analysis identified Streptomycetes in ginseng soil, with three strains inhibiting plant pathogenic fungi. Notably, one strain produced actinomycins, suppressing the ginseng pathogenic fungus Ilyonectria robusta. This research accelerates microbiome application in wild-simulated ginseng cultivation, offering insights into pathogen protection and supporting microbiome utilization in agriculture.

RevDate: 2024-02-20

Sangha JS, Barrett P, Curtis TP, et al (2024)

Effects of glucose and lactate on Streptococcus mutans abundance in a novel multispecies oral biofilm model.

Microbiology spectrum [Epub ahead of print].

The oral microbiome plays an important role in protecting oral health. Here, we established a controlled mixed-species in vitro biofilm model and used it to assess the impact of glucose and lactate on the ability of Streptococcus mutans, an acidogenic and aciduric species, to compete with commensal oral bacteria. A chemically defined medium was developed that supported the growth of S. mutans and four common early colonizers of dental plaque: Streptococcus gordonii, Actinomyces oris, Neisseria subflava, and Veillonella parvula. Biofilms containing the early colonizers were developed in a continuous flow bioreactor, exposed to S. mutans, and incubated for up to 7 days. The abundance of bacteria was estimated by quantitative polymerase chain reaction (qPCR). At high glucose and high lactate, the pH in bulk fluid rapidly decreased to approximately 5.2, and S. mutans outgrew other species in biofilms. In low glucose and high lactate, the pH remained above 5.5, and V. parvula was the most abundant species in biofilms. By contrast, in low glucose and low lactate, the pH remained above 6.0 throughout the experiment, and the microbial community in biofilms was relatively balanced. Fluorescence in situ hybridization confirmed that all species were present in the biofilm and the majority of cells were viable using live/dead staining. These data demonstrate that carbon source concentration is critical for microbial homeostasis in model oral biofilms. Furthermore, we established an experimental system that can support the development of computational models to predict transitions to microbial dysbiosis based on metabolic interactions.IMPORTANCEWe developed a controlled (by removing host factor) dynamic system metabolically representative of early colonization of Streptococcus mutans not measurable in vivo. Hypotheses on factors influencing S. mutans colonization, such as community composition and inoculation sequence and the effect of metabolite concentrations, can be tested and used to predict the effect of interventions such as dietary modifications or the use of toothpaste or mouthwash on S. mutans colonization. The defined in vitro model (species and medium) can be simulated in an in silico model to explore more of the parameter space.

RevDate: 2024-02-20

Schaan AP, Vidal A, Zhang A-N, et al (2024)

Temporal dynamics of gut microbiomes in non-industrialized urban Amazonia.

mSystems [Epub ahead of print].

Increasing levels of industrialization have been associated with changes in gut microbiome structure and loss of features thought to be crucial for maintaining gut ecological balance. The stability of gut microbial communities over time within individuals seems to be largely affected by these changes but has been overlooked among transitioning populations from low- to middle-income countries. Here, we used metagenomic sequencing to characterize the temporal dynamics in gut microbiomes of 24 individuals living an urban non-industrialized lifestyle in the Brazilian Amazon. We further contextualized our data with 165 matching longitudinal samples from an urban industrialized and a rural non-industrialized population. We show that gut microbiome composition and diversity have greater variability over time among non-industrialized individuals when compared to industrialized counterparts and that taxa may present diverse temporal dynamics across human populations. Enterotype classifications show that community types are generally stable over time despite shifts in microbiome structure. Furthermore, by tracking genomes over time, we show that levels of bacterial population replacements are more frequent among Amazonian individuals and that non-synonymous variants accumulate in genes associated with degradation of host dietary polysaccharides. Taken together, our results suggest that the stability of gut microbiomes is influenced by levels of industrialization and that tracking microbial population dynamics is important to understand how the microbiome will adapt to these transitions.IMPORTANCEThe transition from a rural or non-industrialized lifestyle to urbanization and industrialization has been linked to changes in the structure and function of the human gut microbiome. Understanding how the gut microbiomes changes over time is crucial to define healthy states and to grasp how the gut microbiome interacts with the host environment. Here, we investigate the temporal dynamics of gut microbiomes from an urban and non-industrialized population in the Amazon, as well as metagenomic data sets from urban United States and rural Tanzania. We showed that healthy non-industrialized microbiomes experience greater compositional shifts over time compared to industrialized individuals. Furthermore, bacterial strain populations are more frequently replaced in non-industrialized microbiomes, and most non-synonymous mutations accumulate in genes associated with the degradation of host dietary components. This indicates that microbiome stability is affected by transitions to industrialization, and that strain tracking can elucidate the ecological dynamics behind such transitions.

RevDate: 2024-02-20

Hegarty B, Riddell V J, Bastien E, et al (2024)

Benchmarking informatics approaches for virus discovery: caution is needed when combining in silico identification methods.

mSystems [Epub ahead of print].

Understanding the ecological impacts of viruses on natural and engineered ecosystems relies on the accurate identification of viral sequences from community sequencing data. To maximize viral recovery from metagenomes, researchers frequently combine viral identification tools. However, the effectiveness of this strategy is unknown. Here, we benchmarked combinations of six widely used informatics tools for viral identification and analysis (VirSorter, VirSorter2, VIBRANT, DeepVirFinder, CheckV, and Kaiju), called "rulesets." Rulesets were tested against mock metagenomes composed of taxonomically diverse sequence types and diverse aquatic metagenomes to assess the effects of the degree of viral enrichment and habitat on tool performance. We found that six rulesets achieved equivalent accuracy [Matthews Correlation Coefficient (MCC) = 0.77, Padj ≥ 0.05]. Each contained VirSorter2, and five used our "tuning removal" rule designed to remove non-viral contamination. While DeepVirFinder, VIBRANT, and VirSorter were each found once in these high-accuracy rulesets, they were not found in combination with each other: combining tools does not lead to optimal performance. Our validation suggests that the MCC plateau at 0.77 is partly caused by inaccurate labeling within reference sequence databases. In aquatic metagenomes, our highest MCC ruleset identified more viral sequences in virus-enriched (44%-46%) than in cellular metagenomes (7%-19%). While improved algorithms may lead to more accurate viral identification tools, this should be done in tandem with careful curation of sequence databases. We recommend using the VirSorter2 ruleset and our empirically derived tuning removal rule. Our analysis provides insight into methods for in silico viral identification and will enable more robust viral identification from metagenomic data sets.IMPORTANCEThe identification of viruses from environmental metagenomes using informatics tools has offered critical insights in microbial ecology. However, it remains difficult for researchers to know which tools optimize viral recovery for their specific study. In an attempt to recover more viruses, studies are increasingly combining the outputs from multiple tools without validating this approach. After benchmarking combinations of six viral identification tools against mock metagenomes and environmental samples, we found that these tools should only be combined cautiously. Two to four tool combinations maximized viral recovery and minimized non-viral contamination compared with either the single-tool or the five- to six-tool ones. By providing a rigorous overview of the behavior of in silico viral identification strategies and a pipeline to replicate our process, our findings guide the use of existing viral identification tools and offer a blueprint for feature engineering of new tools that will lead to higher-confidence viral discovery in microbiome studies.

RevDate: 2024-02-20

Uddin MJ, Thompson B, Leslie JL, et al (2024)

Investigating the impact of antibiotic-induced dysbiosis on protection from Clostridium difficile colitis by mouse colonic innate lymphoid cells.

mBio [Epub ahead of print].

Innate lymphoid cells (ILCs) play a critical role in maintaining intestinal health in homeostatic and diseased conditions. During Clostridium difficile infection (CDI), IL-33 activates ILC2 to protect from colonic damage and mortality. The function of IL-33 and ILC is tightly regulated by the intestinal microbiota. We set out to determine the impact of antibiotic-induced disruption of the microbiome on ILC function. Our goal was to understand antibiotic-induced changes in ILC function on susceptibility to C. difficile colitis in a mouse model. We utilized high-throughput single-cell RNAseq to investigate the phenotypic features of colonic ILC at baseline, after antibiotic administration with or without IL-33 treatment. We identified a heterogeneous landscape of colonic ILCs with gene signatures of inflammatory, anti-inflammatory, migratory, progenitor, plastic, and antigen-presenting ILCs. Antibiotic treatment decreased ILC2 while coordinately increasing ILC1 and ILC3 phenotypes. Notably, Ifng[+], Ccl5[+], and Il23r[+] ILC increased after antibiotics. IL-33 treatment counteracted the antibiotic effect by downregulating ILC1 and ILC3 and activating ILC2. In addition, IL-33 treatment markedly induced the expression of type 2 genes, including Areg and Il5. Finally, we identified amphiregulin, produced by ILC2, as protective during C. difficile infection. Together, our data expand our understanding of how antibiotics induce susceptibility to C. difficile colitis through their impact on ILC subsets and function.IMPORTANCEClostridium difficile infection (CDI) accounts for around 500,000 symptomatic cases and over 20,000 deaths annually in the United States alone. A major risk factor of CDI is antibiotic-induced dysbiosis of the gut. Microbiota-regulated IL-33 and innate lymphoid cells (ILCs) are important in determining the outcomes of C. difficile infection. Understanding how antibiotic and IL-33 treatment alter the phenotype of colon ILCs is important to identify potential therapeutics. Here, we performed single-cell RNAseq of mouse colon ILCs collected at baseline, after antibiotic treatment, and after IL-33 treatment. We identified heterogeneous subpopulations of all three ILC subtypes in the mouse colon. Our analysis revealed several potential pathways of antibiotic-mediated increased susceptibility to intestinal infection. Our discovery that Areg is abundantly expressed by ILCs, and the protection of mice from CDI by amphiregulin treatment, suggests that the amphiregulin-epidermal growth factor receptor pathway is a potential therapeutic target for treating intestinal colitis.

RevDate: 2024-02-21
CmpDate: 2024-02-21

Shao R, Tan X, Pan M, et al (2024)

Inulin alters gut microbiota to alleviate post-stroke depressive-like behavior associated with the IGF-1-mediated MAPK signaling pathway.

Brain and behavior, 14(1):e3387.

INTRODUCTION: Gut microbiota dysbiosis is a key factor of the pathogenesis of post-stroke depression (PSD). PSD is associated with increased hippocampal neuronal apoptosis and decreased synaptic connectivity. Inulin can be involved in hippocampal neuron protection through the microbiome-gut-brain axis. However, the neuroprotective effects of inulin in PSD are still to be further investigated.

METHODS: By utilizing the GEO public database, we identify differentially expressed genes in the hippocampus following inulin intake. This can help us discover key signaling pathways through functional enrichment analysis. Furthermore, we validate the expression levels of signaling molecules in a rat model of PSD and examine the effects of inulin on behavioral changes and body weight. Additionally, conducting a microbiome analysis to identify significantly different microbial populations and perform correlation analysis.

RESULTS: The intake of inulin significantly up-regulated mitogen-activated protein kinase signaling pathway in the hippocampus. Inulin changed in the gut microbiota structure, leading to an increase in the abundance of Lactobacillus and Clostridium_sensu_stricto_1 in the intestines of PSD rats, while decreasing the abundance of Ruminococcus UCG_005, Prevotella_9, Oscillospiraceae, and Clostridia UCG_014. Furthermore, the inulin diet elevated levels of insulin-like growth factor 1 in the serum, which showed a positive correlation with the abundance of Lactobacillus. Notably, the consumption of inulin-enriched diet increased activity levels and preference for sugar water in PSD rats, while also reducing body weight.

CONCLUSION: These findings highlight the potential therapeutic benefits of inulin in the management of depression and emphasize the importance of maintaining a healthy gut microbiota for PSD.

RevDate: 2024-02-21
CmpDate: 2024-02-21

Reuter MA, Tucker M, Marfori Z, et al (2024)

Dietary resistant starch supplementation increases gut luminal deoxycholic acid abundance in mice.

Gut microbes, 16(1):2315632.

Bile acids (BA) are among the most abundant metabolites produced by the gut microbiome. Primary BAs produced in the liver are converted by gut bacterial 7-α-dehydroxylation into secondary BAs, which can differentially regulate host health via signaling based on their varying affinity for BA receptors. Despite the importance of secondary BAs in host health, the regulation of 7-α-dehydroxylation and the role of diet in modulating this process is incompletely defined. Understanding this process could lead to dietary guidelines that beneficially shift BA metabolism. Dietary fiber regulates gut microbial composition and metabolite production. We tested the hypothesis that feeding mice a diet rich in a fermentable dietary fiber, resistant starch (RS), would alter gut bacterial BA metabolism. Male and female wild-type mice were fed a diet supplemented with RS or an isocaloric control diet (IC). Metabolic parameters were similar between groups. RS supplementation increased gut luminal deoxycholic acid (DCA) abundance. However, gut luminal cholic acid (CA) abundance, the substrate for 7-α-dehydroxylation in DCA production, was unaltered by RS. Further, RS supplementation did not change the mRNA expression of hepatic BA producing enzymes or ileal BA transporters. Metagenomic assessment of gut bacterial composition revealed no change in the relative abundance of bacteria known to perform 7-α-dehydroxylation. P. ginsenosidimutans and P. multiformis were positively correlated with gut luminal DCA abundance and increased in response to RS supplementation. These data demonstrate that RS supplementation enriches gut luminal DCA abundance without increasing the relative abundance of bacteria known to perform 7-α-dehydroxylation.

RevDate: 2024-02-21

Gao Q, Liu JH, Ma WY, et al (2024)

Genomics-Microbiome Based Assessment of Bidirectional Causality Between Gut Microbiota and Psoriasis.

Clinical, cosmetic and investigational dermatology, 17:435-445.

BACKGROUND: Traditional observational studies have found a possible risk association of the gut microbiota for psoriasis. Meanwhile, psoriasis may also affect the changes in the gut microbiota. However, the available evidence does not demonstrate a reciprocal relationship between the gut microbiota and psoriasis. This limits our understanding on the role of the gut microbiota in the mechanisms of psoriasis.

METHODS: To address this question we used Mendelian randomization, a novel epidemiological approach, and acquired the largest current gut microbiota GWAS data from the MiBioGen consortium as well as psoriasis GWAS data from the FinnGen consortium, and performed two-sample bidirectional MR analyses using a multiple MR analysis approach. Finally, the robustness of the results was assessed by sensitivity analysis.

RESULTS: Our results indicate that five bacterial genera are causally related to psoriasis and psoriasis is causally related to four bacterial genera.

CONCLUSION: These results suggest a bidirectional causal influence of psoriasis on the gut microbiota. Our results somewhat challenge the causal inferences of previous observational studies. We found that the specific bacterial genera with a risk effect on psoriasis were different from those found to characterize psoriasis in previous observational studies, and that these psoriasis-characterizing genera were inversely associated with psoriasis.

RevDate: 2024-02-21

Peeters J, Bot DM, Rovelo Ruiz G, et al (2024)

Snowflake: visualizing microbiome abundance tables as multivariate bipartite graphs.

Frontiers in bioinformatics, 4:1331043.

Current visualizations in microbiome research rely on aggregations in taxonomic classifications or do not show less abundant taxa. We introduce Snowflake: a new visualization method that creates a clear overview of the microbiome composition in collected samples without losing any information due to classification or neglecting less abundant reads. Snowflake displays every observed OTU/ASV in the microbiome abundance table and provides a solution to include the data's hierarchical structure and additional information obtained from downstream analysis (e.g., alpha- and beta-diversity) and metadata. Based on the value-driven ICE-T evaluation methodology, Snowflake was positively received. Experts in microbiome research found the visualizations to be user-friendly and detailed and liked the possibility of including and relating additional information to the microbiome's composition. Exploring the topological structure of the microbiome abundance table allows them to quickly identify which taxa are unique to specific samples and which are shared among multiple samples (i.e., separating sample-specific taxa from the core microbiome), and see the compositional differences between samples. An R package for constructing and visualizing Snowflake microbiome composition graphs is available at

RevDate: 2024-02-21

Shi S, Chu Y, Liu H, et al (2024)

Predictable regulation of survival by intratumoral microbe-immune crosstalk in patients with lung adenocarcinoma.

Microbial cell (Graz, Austria), 11:29-40.

Intratumoral microbiota can regulate the tumor immune microenvironment (TIME) and mediate tumor prognosis by promoting inflammatory response or inhibiting anti-tumor effects. Recent studies have elucidated the potential role of local tumor microbiota in the development and progression of lung adenocarcinoma (LUAD). However, whether intratumoral microbes are involved in the TIME that mediates the prognosis of LUAD remains unknown. Here, we obtained the matched tumor microbiome and host transcriptome and survival data of 478 patients with LUAD in The Cancer Genome Atlas (TCGA). Machine learning models based on immune cell marker genes can predict 1- to 5-year survival with relative accuracy. Patients were stratified into high- and low-survival-risk groups based on immune cell marker genes, with significant differences in intratumoral microbial communities. Specifically, patients in the high-risk group had significantly higher alpha diversity (p < 0.05) and were characterized by an enrichment of lung cancer-related genera such as Streptococcus. However, network analysis highlighted a more active pattern of dominant bacteria and immune cell crosstalk in TIME in the low-risk group compared to the high-risk group. Our study demonstrated that intratumoral microbiota-immune crosstalk was strongly associated with prognosis in LUAD patients, which would provide new targets for the development of precise therapeutic strategies.

RevDate: 2024-02-21

Monday L, Tillotson G, T Chopra (2024)

Microbiota-Based Live Biotherapeutic Products for Clostridioides Difficile Infection- The Devil is in the Details.

Infection and drug resistance, 17:623-639.

Clostridioides difficile infection (CDI) remains a significant contributor to healthcare costs and morbidity due to high rates of recurrence. Currently, available antibiotic treatment strategies further disrupt the fecal microbiome and do not address the alterations in commensal flora (dysbiosis) that set the stage for CDI. Advances in microbiome-based research have resulted in the development of new agents, classified as live biotherapeutic products (LBPs), for preventing recurrent CDI (rCDI) by restoring eubiosis. Prior to the LBPs, fecal microbiota transplantation (FMT) was available for this purpose; however, lack of large-scale availability and safety concerns have remained barriers to its widespread use. The LBPs are an exciting development, but questions remain. Some are derived directly from human stool while other developmental products contain a defined microbial consortium manufactured ex vivo, and they may be composed of either living bacteria or their spores, making it difficult to compare members of this heterogenous drug class to one another. None have been studied head-to head or against FMT in preventing rCDI. As a class, they have considerable variability in their biologic composition, biopharmaceutic science, route of administration, stages of development, and clinical trial data. This review will start by explaining the role of dysbiosis in CDI, then give the details of the biopharmaceutical components for the LBPs which are approved or in development including how they differ from FMT and from one another. We then discuss the clinical trials of the LBPs currently approved for rCDI and end with the future clinical directions of LBPs beyond C. difficile.

RevDate: 2024-02-21

Mihai MM, Popa MI, Holban AM, et al (2023)

Clinical and microbiological features of host-bacterial interplay in chronic venous ulcers versus other types of chronic skin ulcers.

Frontiers in microbiology, 14:1326904.

INTRODUCTION: Chronic venous ulcers of the lower limbs develop in the context of advanced venous disease and have a significant impact on the patient's quality of life, being associated with depression and worrisome suicide rates, as well as with an economic burden caused by increased medical care costs and high epidemiological risks of healthcare associated infections and emergence of strains resistant to multiple classes of antibiotics and/ or antiseptics. Although numerous studies have investigated the composition of the chronic wounds microbiome, either by culture-dependent or independent methods, there are no data on the association between virulence and resistance profiles of strains isolated from venous ulcers and the clinical picture of this pathology. The elucidation of pathogenic mechanisms, at both phenotypic and molecular level, is crucial in the fight against these important human microbial agents, in order to develop novel biomarkers and discover new therapeutic targets.

METHODS: In this study we aimed to characterize the phenotypic virulence profiles (including the ability to develop biofilms) of microorganisms isolated from chronic skin wounds and to correlate them with the clinical symptomatology. Considering the high incidence of Staphylococcus aureus infections in chronic ulcers, but also the ability of this species to develop multi-drug resistance, we performed an more in-depth study of the phenotypic and genotypic virulence profiles of methicillin-resistant Staphylococcus.

RESULTS: The study revealed important differences regarding the clinical evolution and virulence profiles of microorganisms isolated from lower limb wounds, as well as between patients diagnosed with chronic venous ulcers and those with lesions of different etiology.

RevDate: 2024-02-21

Zhang XE, Zheng P, Ye SZ, et al (2024)

Microbiome: Role in Inflammatory Skin Diseases.

Journal of inflammation research, 17:1057-1082.

As the body's largest organ, the skin harbors a highly diverse microbiota, playing a crucial role in resisting foreign pathogens, nurturing the immune system, and metabolizing natural products. The dysregulation of human skin microbiota is implicated in immune dysregulation and inflammatory responses. This review delineates the microbial alterations and immune dysregulation features in common Inflammatory Skin Diseases (ISDs) such as psoriasis, rosacea, atopic dermatitis(AD), seborrheic dermatitis(SD), diaper dermatitis(DD), and Malassezia folliculitis(MF).The skin microbiota, a complex and evolving community, undergoes changes in composition and function that can compromise the skin microbial barrier. These alterations induce water loss and abnormal lipid metabolism, contributing to the onset of ISDs. Additionally, microorganisms release toxins, like Staphylococcus aureus secreted α toxins and proteases, which may dissolve the stratum corneum, impairing skin barrier function and allowing entry into the bloodstream. Microbes entering the bloodstream activate molecular signals, leading to immune disorders and subsequent skin inflammatory responses. For instance, Malassezia stimulates dendritic cells(DCs) to release IL-12 and IL-23, differentiating into a Th17 cell population and producing proinflammatory mediators such as IL-17, IL-22, TNF-α, and IFN-α.This review offers new insights into the role of the human skin microbiota in ISDs, paving the way for future skin microbiome-specific targeted therapies.

RevDate: 2024-02-21

McLaughlin MS, Yurgel SN, Abbasi PA, et al (2024)

The effects of chemical fungicides and salicylic acid on the apple microbiome and fungal disease incidence under changing environmental conditions.

Frontiers in microbiology, 15:1342407.

Epiphytic and endophytic micro-organisms associated with plants form complex communities on or in their host plant. These communities influence physiological traits, development, and host susceptibility to abiotic and biotic stresses, and these communities are theorized to have evolved alongside their hosts, forming a unit of selection known as the holobiont. The microbiome is highly variable and can be influenced by abiotic factors, including applied exogenous agents. In this study, we compared the impact of chemical fungicide and salicylic acid treatments on the fungal communities of "Honeycrisp" apples at harvest over two consecutive growing years. We demonstrated variations in fungal community structure and composition by tissue type, growing season, and treatment regimes and that fungicide treatments were associated with reduced network complexity. Finally, we show that the inclusion of salicylic acid with 50% less chemical fungicides in an integrated spray program allowed a reduction in fungicide use while maintaining effective control of disease at harvest and following storage.

RevDate: 2024-02-21

Mazel F, Pitteloud C, Guisan A, et al (2024)

Contrasted host specificity of gut and endosymbiont bacterial communities in alpine grasshoppers and crickets.

ISME communications, 4(1):ycad013.

Bacteria colonize the body of macroorganisms to form associations ranging from parasitic to mutualistic. Endosymbiont and gut symbiont communities are distinct microbiomes whose compositions are influenced by host ecology and evolution. Although the composition of horizontally acquired symbiont communities can correlate to host species identity (i.e. harbor host specificity) and host phylogeny (i.e. harbor phylosymbiosis), we hypothesize that the microbiota structure of vertically inherited symbionts (e.g. endosymbionts like Wolbachia) is more strongly associated with the host species identity and phylogeny than horizontally acquired symbionts (e.g. most gut symbionts). Here, using 16S metabarcoding on 336 guts from 24 orthopteran species (grasshoppers and crickets) in the Alps, we observed that microbiota correlated to host species identity, i.e. hosts from the same species had more similar microbiota than hosts from different species. This effect was ~5 times stronger for endosymbionts than for putative gut symbionts. Although elevation correlated with microbiome composition, we did not detect phylosymbiosis for endosymbionts and putative gut symbionts: closely related host species did not harbor more similar microbiota than distantly related species. Our findings indicate that gut microbiota of studied orthopteran species is more correlated to host identity and habitat than to the host phylogeny. The higher host specificity in endosymbionts corroborates the idea that-everything else being equal-vertically transmitted microbes harbor stronger host specificity signal, but the absence of phylosymbiosis suggests that host specificity changes quickly on evolutionary time scales.

RevDate: 2024-02-21
CmpDate: 2024-02-21

Gerasimidis K, Russell RK, Giachero F, et al (2024)

Precision nutrition in pediatric IBD: A position paper from the ESPGHAN special interest group for basic science and translational research, the IBD Porto group, and allied health professionals.

Journal of pediatric gastroenterology and nutrition, 78(2):428-445.

Stratified and precision nutrition refers to disease management or prevention of disease onset, based on dietary interventions tailored to a person's characteristics, biology, gut microbiome, and environmental exposures. Such treatment models may lead to more effective management of inflammatory bowel disease (IBD) and reduce risk of disease development. This societal position paper aimed to report advances made in stratified and precision nutritional therapy in IBD. Following a structured literature search, limited to human studies, we identified four relevant themes: (a) nutritional epidemiology for risk prediction of IBD development, (b) food-based dietary interventions in IBD, (c) exclusive enteral nutrition (EEN) for Crohn's disease (CD) management, and (d) pre- and probiotics for IBD management. There is scarce literature upon which we can make recommendations for precision or stratified dietary therapy for IBD, both for risk of disease development and disease management. Certain single-nucleotide polymorphisms related to polyunsaturated fatty acid (PUFA) metabolism may modify the effect dietary PUFA have in increasing the risk of IBD development. Non-colonic CD, mild-to-moderate CD, and high microbiota richness may predict success of EEN and may be used both for prediction of treatment continuation, but also for early cessation in nonresponders. There is currently insufficient evidence to make recommendations for precision or stratified dietary therapy for patients with established IBD. Despite the great interest in stratified and precision nutrition, we currently lack data to support conclusive recommendations. Replication of early findings by independent research groups and within structured clinical interventions is required.

RevDate: 2024-02-21
CmpDate: 2024-02-21

Buiatte V, Fonseca A, Alonso Madureira P, et al (2024)

A comparative study of the bacterial diversity and composition of nursery piglets' oral fluid, feces, and housing environment.

Scientific reports, 14(1):4119.

The oral cavity is the portal of entry for many microorganisms that affect swine, and the swine oral fluid has been used as a specimen for the diagnosis of several infectious diseases. The oral microbiota has been shown to play important roles in humans, such as protection against non-indigenous bacteria. In swine, studies that have investigated the microbial composition of the oral cavity of pigs are scarce. This study aimed to characterize the oral fluid microbiota of weaned pigs from five commercial farms in Brazil and compare it to their respective fecal and environmental microbiotas. Bacterial compositions were determined by 16S rRNA gene sequencing and analyzed in R Studio. Oral fluid samples were significantly less diverse (alpha diversity) than pen floor and fecal samples (P < 0.01). Alpha diversity changed among farms in oral fluid and pen floor samples, but no differences were observed in fecal samples. Permutational ANOVA revealed that beta diversity was significantly different among sample types (P = 0.001) and farms (P = 0.001), with separation of sample types (feces, pen floor, and oral fluid) on the principal coordinates analysis. Most counts obtained from oral fluid samples were classified as Firmicutes (80.4%) and Proteobacteria (7.7%). The genera Streptococcus, members of the Pasteurellaceae family, and Veillonella were differentially abundant in oral fluid samples when compared to fecal samples, in which Streptococcus was identified as a core genus that was strongly correlated (SparCC) with other taxa. Firmicutes and Bacteroidota were the most relatively abundant phyla identified in fecal and pen floor samples, and Prevotella_9 was the most classified genus. No differentially abundant taxa were identified when comparing fecal samples and pen floor samples. We concluded that under the conditions of our study, the oral fluid microbiota of weaned piglets is different (beta diversity) and less diverse (alpha diversity) than the fecal and environmental microbiotas. Several differentially abundant taxa were identified in the oral fluid samples, and some have been described as important colonizers of the oral cavity in human microbiome studies. Further understanding of the relationship between the oral fluid microbiota and swine is necessary and would create opportunities for the development of innovative solutions that target the microbiota to improve swine health and production.

RevDate: 2024-02-19

Bajaj A, Markandey M, Kedia S, et al (2024)

Gut bacteriome in inflammatory bowel disease: An update on recent advances.

Indian journal of gastroenterology : official journal of the Indian Society of Gastroenterology [Epub ahead of print].

Inflammatory bowel diseases (IBD) are chronic inflammatory gut disorders, majorly classified as ulcerative colitis and Crohn's disease. The complex, multifactorial etiopathogenesis of IBD involves genetic predisposition, environmental cues, aberrant mucosal immune response and a disturbed gut microbiota. Epidemiological trends, studies in gnotobiotic mice models and genome-wide association studies, identifying genes involved in microbial handling, together mount evidence in support of the gut microbiota playing a pivotal role in IBD pathogenesis. Both Crohn's disease and ulcerative colitis are characterized by severe dysbiosis of the gut microbiome, marked by an expansion of detrimental taxa and concomitant depletion of beneficial members. IBD is characterized by reduction in abundances of bacterial genera involved in production of short-chain fatty acids, bio-transformations of bile acids and synthesis of indole-based tryptophan compounds such as Faecalibacterium, Ruminococcus, Coprococcus, Dorea, Parabacteroides, Eubacterium, Oscillibacter and Prevotella and elevation in members of phyla Proteobacteria and Actinobacteria. This imbalance not only results in exaggerated immune signaling towards the microbial antigens, but also results in an altered metabolomic milieu that triggers additional inflammatory cascades. The present review provides insights into the bacterial dysbiosis observed across different intestinal sites and their metabolomic imprints participating in IBD.

RevDate: 2024-02-21
CmpDate: 2024-02-21

Spohr P, Scharf S, Rommerskirchen A, et al (2024)

Insights into gut microbiomes in stem cell transplantation by comprehensive shotgun long-read sequencing.

Scientific reports, 14(1):4068.

The gut microbiome is a diverse ecosystem, dominated by bacteria; however, fungi, phages/viruses, archaea, and protozoa are also important members of the gut microbiota. Exploration of taxonomic compositions beyond bacteria as well as an understanding of the interaction between the bacteriome with the other members is limited using 16S rDNA sequencing. Here, we developed a pipeline enabling the simultaneous interrogation of the gut microbiome (bacteriome, mycobiome, archaeome, eukaryome, DNA virome) and of antibiotic resistance genes based on optimized long-read shotgun metagenomics protocols and custom bioinformatics. Using our pipeline we investigated the longitudinal composition of the gut microbiome in an exploratory clinical study in patients undergoing allogeneic hematopoietic stem cell transplantation (alloHSCT; n = 31). Pre-transplantation microbiomes exhibited a 3-cluster structure, characterized by Bacteroides spp. /Phocaeicola spp., mixed composition and Enterococcus abundances. We revealed substantial inter-individual and temporal variabilities of microbial domain compositions, human DNA, and antibiotic resistance genes during the course of alloHSCT. Interestingly, viruses and fungi accounted for substantial proportions of microbiome content in individual samples. In the course of HSCT, bacterial strains were stable or newly acquired. Our results demonstrate the disruptive potential of alloHSCTon the gut microbiome and pave the way for future comprehensive microbiome studies based on long-read metagenomics.

RevDate: 2024-02-19

Zhang C, van der Heijden MGA, Dodds BK, et al (2024)

Correction: A tripartite bacterial-fungal-plant symbiosis in the mycorrhiza-shaped microbiome drives plant growth and mycorrhization.

Microbiome, 12(1):30.

RevDate: 2024-02-21
CmpDate: 2024-02-21

Bazzani D, Heidrich V, Manghi P, et al (2024)

Favorable subgingival plaque microbiome shifts are associated with clinical treatment for peri-implant diseases.

NPJ biofilms and microbiomes, 10(1):12.

We performed a longitudinal shotgun metagenomic investigation of the plaque microbiome associated with peri-implant diseases in a cohort of 91 subjects with 320 quality-controlled metagenomes. Through recently improved taxonomic profiling methods, we identified the most discriminative species between healthy and diseased subjects at baseline, evaluated their change over time, and provided evidence that clinical treatment had a positive effect on plaque microbiome composition in patients affected by mucositis and peri-implantitis.

RevDate: 2024-02-21
CmpDate: 2024-02-21

Reay WR, Kiltschewskij DJ, Di Biase MA, et al (2024)

Genetic influences on circulating retinol and its relationship to human health.

Nature communications, 15(1):1490.

Retinol is a fat-soluble vitamin that plays an essential role in many biological processes throughout the human lifespan. Here, we perform the largest genome-wide association study (GWAS) of retinol to date in up to 22,274 participants. We identify eight common variant loci associated with retinol, as well as a rare-variant signal. An integrative gene prioritisation pipeline supports novel retinol-associated genes outside of the main retinol transport complex (RBP4:TTR) related to lipid biology, energy homoeostasis, and endocrine signalling. Genetic proxies of circulating retinol were then used to estimate causal relationships with almost 20,000 clinical phenotypes via a phenome-wide Mendelian randomisation study (MR-pheWAS). The MR-pheWAS suggests that retinol may exert causal effects on inflammation, adiposity, ocular measures, the microbiome, and MRI-derived brain phenotypes, amongst several others. Conversely, circulating retinol may be causally influenced by factors including lipids and serum creatinine. Finally, we demonstrate how a retinol polygenic score could identify individuals more likely to fall outside of the normative range of circulating retinol for a given age. In summary, this study provides a comprehensive evaluation of the genetics of circulating retinol, as well as revealing traits which should be prioritised for further investigation with respect to retinol related therapies or nutritional intervention.

RevDate: 2024-02-21
CmpDate: 2024-02-21

Qiu C, Zhou W, Shen H, et al (2024)

Profiles of subgingival microbiomes and gingival crevicular metabolic signatures in patients with amnestic mild cognitive impairment and Alzheimer's disease.

Alzheimer's research & therapy, 16(1):41.

BACKGROUND: The relationship between periodontitis and Alzheimer's disease (AD) has attracted more attention recently, whereas profiles of subgingival microbiomes and gingival crevicular fluid (GCF) metabolic signatures in AD patients have rarely been characterized; thus, little evidence exists to support the oral-brain axis hypothesis. Therefore, our study aimed to characterize both the microbial community of subgingival plaque and the metabolomic profiles of GCF in patients with AD and amnestic mild cognitive impairment (aMCI) for the first time.

METHODS: This was a cross-sectional study. Clinical examinations were performed on all participants. The microbial community of subgingival plaque and the metabolomic profiles of GCF were characterized using the 16S ribosomal RNA (rRNA) gene high-throughput sequencing and liquid chromatography linked to tandem mass spectrometry (LC-MS/MS) analysis, respectively.

RESULTS: Thirty-two patients with AD, 32 patients with aMCI, and 32 cognitively normal people were enrolled. The severity of periodontitis was significantly increased in AD patients compared with aMCI patients and cognitively normal people. The 16S rRNA gene sequencing results showed that the relative abundances of 16 species in subgingival plaque were significantly correlated with cognitive function, and LC-MS/MS analysis identified a total of 165 differentially abundant metabolites in GCF. Moreover, multiomics Data Integration Analysis for Biomarker discovery using Latent cOmponents (DIABLO) analysis revealed that 19 differentially abundant metabolites were significantly correlated with Veillonella parvula, Dialister pneumosintes, Leptotrichia buccalis, Pseudoleptotrichia goodfellowii, and Actinomyces massiliensis, in which galactinol, sn-glycerol 3-phosphoethanolamine, D-mannitol, 1 h-indole-1-pentanoic acid, 3-(1-naphthalenylcarbonyl)- and L-iditol yielded satisfactory accuracy for the predictive diagnosis of AD progression.

CONCLUSIONS: This is the first combined subgingival microbiome and GCF metabolome study in patients with AD and aMCI, which revealed that periodontal microbial dysbiosis and metabolic disorders may be involved in the etiology and progression of AD, and the differential abundance of the microbiota and metabolites may be useful as potential markers for AD in the future.

RevDate: 2024-02-20

Sheta B, Waheed O, Ayad E, et al (2024)

Constitutive immunity is influenced by avian influenza virus-induced modification of gut microbiota in Eurasian teal (Anas crecca).

Comparative biochemistry and physiology. Toxicology & pharmacology : CBP, 278:109867 pii:S1532-0456(24)00035-8 [Epub ahead of print].

Understanding the dynamics of migrant birds' gut microbial communities is essential for evaluating their ecological interactions, since these birds act as vectors for zoonotic viruses and their gut microbiome may have exceptional relationship with zoonotic viral infection. The Eurasian teal duck Anas crecca traverses continents during migration, combining and providing intercontinental links for avian influenza viruses (AIV) of different origins. The present study aimed to investigate how the AIV infection affects gut microbial composition and evaluate the consequent physiological stress and constitutive immunity of teal birds. Samples were collected from 2 flocks during their migratory stopover in northern Egypt. An important shift in gut microbiota of AIV-infected individuals has been detected by RT-PCR. In healthy teal, firmicutes dominated followed by proteobacteria, while the structure was reversed in infected birds. Infection with AIV significantly increased the stress hormone corticosterone, accompanied by a significant increase in both oxidative stress markers and antioxidants. Constitutive immunity, measured by plasma bactericidal effect against E. coli, the nonspecific natural antibodies, and the mediated complement activation, was reduced in AIV-infected teal birds. Constitutive immunity parameters were proportionally correlated to the firmicutes and inversely to the proteobacteria abundances, but not to the viral positivity. In conclusion, the present study provides initial evidence of the alteration of the gut microbiome in the Eurasian teal Anas crecca by AIV infection and demonstrates that the AIV-induced reduction in constitutive immunity is a consequence of the shift in microbiome composition rather than the virus infection itself or its induced stress.

RevDate: 2024-02-19

Li X, Wang Y, Sun H, et al (2024)

Differences in ingestion and biodegradation of the melamine formaldehyde plastic by yellow mealworms Tenebrio molitor and superworms Zophobas atratus, and the prediction of functional gut microbes.

Chemosphere pii:S0045-6535(24)00392-8 [Epub ahead of print].

Plastics biodegradation by insect larvae is considered as a new strategy for plastic wastes treatment. To uncover the biodegradation of a more complex chemical polymer of melamine formaldehyde (MF) by insect larvae, two worm species of yellow mealworm Tenebrio molitor and superworm Zophobas atratus were fed on MF foam as sole diet for 45 days with sole bran diet as control. Although the MF foam consumption by yellow mealworms of 0.38 mg/d/g-larvae was almost 40% higher than that by superworms of 0.28 mg/d/g-larvae, a similar decreasing of survival rates in both species were obtained at about 58%, indicating the adverse effects on their growth. Depolymerization and biodegradation of MF foam occurred in both larval guts, but was more extensive in yellow mealworms. MF foam sole diets influenced gut bacterial and fungal microbiomes of both larvae species, which were assessed by Illumina MiSeq on day 45. Compared to the bran-fed group, both gut bacterial and fungal communities significantly changed in MF-fed groups, but differed in the two larvae species. The results demonstrated a strong association between the distinctive gut microbiome and MF foam degradation, such as unclassified Enterobacteriaceae, Hyphopichia and Issatchenkia. However, sole MF foam diet negatively influenced worms, like lower survival rates and gut abnormalities. In summary, MF foam could be degraded by both yellow mealworms and superworms, albeit with adverse effects. Gut microbes were strongly associated to MF foam degradation, especially the gut fungi.

RevDate: 2024-02-19

Han S, Li Z, Shi Y, et al (2024)

11-Plex DiLeu Isobaric Labeling Enables Quantitative Assessment of Brain Region Protein Association Networks Impacted by the Gut Microbiome.

Analytical chemistry [Epub ahead of print].

Gut microbiota can regulate host brain functions and influence various physiological and pathological processes through the brain-gut axis. To systematically elucidate the intervention of different gut environments on different brain regions, we implemented an integrated approach that combines 11-plex DiLeu isobaric tags with a "BRIDGE" normalization strategy to comparatively analyze the proteome of six brain regions in germ-free (GF)- and conventionally raised (ConvR)-mice. A total of 5945 proteins were identified and 5656 were quantifiable, while 1906 of them were significantly changed between GF- and ConvR-mice; 281 proteins were filtered with FC greater than 1.2 in at least one brain region, of which heatmap analysis showed clear protein profile disparities, both between brain regions and gut microbiome conditions. Gut microbiome impact is most overt in the hypothalamus and the least in the thalamus region. Collectively, this approach allows an in-depth investigation of the induced protein changes by multiple gut microbiome environments in a brain region-specific manner. This comprehensive proteomic work improves the understanding of the brain region protein association networks impacted by the gut microbiome and highlights the critical roles of the brain-gut axis.

RevDate: 2024-02-19

Rithidech KN, Peanlikhit T, Honikel L, et al (2024)

Consumption of Apigenin Prevents Radiation-induced Gut Dysbiosis in Male C57BL/6J Mice Exposed to Silicon Ions.

Radiation research pii:499043 [Epub ahead of print].

The search for medical treatments to prevent radiation-induced damage to gastrointestinal tissue is crucial as such injuries can be fatal. This study aimed to investigate the effects of apigenin (AP) on the gut microbiome of irradiated mice, as it is a promising radiation countermeasure. Male C57BL/6J mice were divided into four groups, with six mice in each group. Two groups were given food with apigenin (20 mg/kg body weight or AP 20) before and after exposure to 0 or 50 cGy of silicon (28Si) ions, while another two groups of mice received regular diet without apigenin (0 mg/kg body weight or AP 0) before and after irradiation. The duodenum, the primary site for oral AP absorption, was collected from each mouse seven days after radiation exposure. Using 16S rRNA amplicon sequencing, we found significant differences in microbial diversity among groups. Firmicutes and Bacteroidetes were the major phyla for all groups, while actinobacterial and proteobacterial sequences represented only a small percentage. Mice not given dietary apigenin had a higher Firmicutes and Bacteroidetes (F/B) ratio and an imbalanced duodenal microbiota after exposure to radiation, while irradiated mice given apigenin had maintained homeostasis of the microbiota. Additionally, irradiated mice not given apigenin had decreased probiotic bacteria abundance and increased inflammation, while apigenin-supplemented mice had reduced inflammation and restored normal histological structure. In conclusion, our results demonstrate the potential of dietary apigenin as a countermeasure against radiation-induced gut injuries due to its anti-inflammatory activity, reduction of gut microbiota dysbiosis, and increase in probiotic bacteria (e.g., Lachnospiraceae, Muribaculaceae and Bifidobacteriaceae).

RevDate: 2024-02-21
CmpDate: 2024-02-20

Abou Chacra L, Bonnet M, Heredia M, et al (2024)

Peptoniphilus genitalis sp. nov. and Mobiluncus massiliensis sp. nov.: Novel Bacteria Isolated from the Vaginal Microbiome.

Current microbiology, 81(4):97.

The strains Marseille-Q7072[T] (= CSUR Q7072[T] = CECT 30604[ T]) and Marseille-Q7826[T] (= CSUR Q7826[T] = CECT 30727[ T]) were isolated from vaginal samples. As MALDI-TOF mass spectrometry failed to identify them, their genomes were directly sequenced to determine their taxogenomic identities. Both strains are anaerobic without any oxidase and catalase activity. C16:0 is the most abundant fatty acid for both strains. Strain Marseille-Q7072[T] is non-spore-forming, non-motile, Gram-stain-positive, and coccus-shaped, while strain Marseille-Q7826[T] is non-spore-forming, motile, Gram-stain-variable, and curved rod-shaped. The genomic comparison of the Marseille-Q7072[T] and Marseille-Q7826[T] strains showed that all digital DNA-DNA hybridisation (dDDH) and mean orthologous nucleotide identity (OrthoANI) values were below published species thresholds (70% and 95-96%, respectively) with other closely related species with standing in nomenclature. Thus, we conclude that both strains are new bacterial species. Strain Marseille-Q7072[T] is a new member of the Bacillota phylum, for which the name Peptoniphilus genitalis sp. nov. is proposed, while the Marseille-Q7826[T] strain is a new member of the Actinomycetota phylum, for which the name Mobiluncus massiliensis sp. nov. is proposed.

RevDate: 2024-02-20
CmpDate: 2024-02-20

Sun X, Han B, Han Q, et al (2024)

Similarity of Chinese and Pakistani oral microbiome.

Antonie van Leeuwenhoek, 117(1):38.

Oral microbiota is vital for human health and can be affected by various factors (i.e. diets, ethnicity). However, few studies have compared oral microbiota of individuals from different nationalities in the same environment. Here, we explored the assembly and interaction of oral microbial communities of Chinese and Pakistanis in one university. Firmicutes and Proteobacteria were the predominant microorganisms in the oral cavity of Chinese and Pakistanis. Streptococcus and Neisseria were the dominant genera of China, while Streptococcus and Haemophilus were the dominant genera of Pakistanis. In addition, the oral community membership and structure were not influenced by season, Chinese/Pakistani student and gender, reflecting the stability of the human oral microbiome. The beta diversity of oral microbiomes between Chinese and Pakistanis significantly differed in winter, but not in spring. The alpha diversity of Chinese students and Pakistani students was similar. Moreover, oral microbial community of both Chinese and Pakistani students was mainly driven by stochastic processes. The microbial network of Chinese was more complexity and stability than that of Pakistanis. Our study uncovers the characteristics of human oral microbiota, which is of great significance for oral and human health.

RevDate: 2024-02-19

Smulders T, Reitsma S, CM van Drunen (2024)

Microbiome analyses in chronic rhinosinusitis.

Rhinology pii:3160 [Epub ahead of print].

In this edition of Rhinology we feature the work of Connell and colleagues from Australia on chronic rhinosinusitis that describes an interesting new pipeline to characterize the bacterial composition of microbiota. We are constantly exposed to a multitude of micro-organisms in the environment and our immune system has the important task discerning and fighting off potential threats. In most people the immune system is doing its job properly and prevents anything untoward from happening. On occasion, a microbe slips by the first (innate) level of defense and we might suffer from an infection. This then activates the second layer of (the adaptive) defense tasked to clear this infection. Sometimes the immune system gets its wrong and starts a full-out defense against something harmless, and an allergy is born. The task of the immune system of doing what is right is even more difficult than it might seem at first sight. In addition to these incidental potential threats, our mucosal surfaces are lined with commensal bacteria which contributes to the complexity of our environment. This collection of bacteria or microbiome has become a major focus of research, as the composition of this microbiome seems related to the health state of the individual. Originally the relationship between the gut microbiome and the development of asthma and allergy was the main focus. In recent years, the focus has been broadened to include the microbiome of the upper and lower airways. In addition to allergy, our field has also been given more and more attention to studying the microbiome in chronic rhinosinusitis.

RevDate: 2024-02-19

Delong LM, Witt CE, Pennell M, et al (2024)

A microfluidic chip for sustained oxygen gradient formation in the intestine ex vivo.

Lab on a chip [Epub ahead of print].

The oxygen gradient across the intestine influences intestinal physiology and the microbial environment of the microbiome. The microbiome releases metabolites that communicate with enterochromaffin cells, neuronal cells, and resident immune cells to facilitate the bidirectional communication across the gut-brain axis. Measuring communication between various cell types within the intestine could provide essential information about key regulators of gut and brain health; however, the microbial environment of the intestine is heavily dependent on the physiological oxygen gradient that exists across the intestinal wall. Likewise, there exist a need for methods which enable real-time monitoring of intestinal signaling ex vivo yet this remains challenging due to the inability to adequately culture intestinal tissue ex vivo while also exposing the appropriate locations of the intestine for probe insertion and monitoring. Here, we designed and fabricated a 3D printed microfluidic device to maintain the oxygen gradient across precision cut murine intestinal slices with the capability to couple to external neurochemical recording techniques. The gradient is maintained from outlets below while allowing access to the slice from above for detection with fast scan cyclic voltammetry (FSCV) and carbon-fiber microelectrodes. A series of 11 outlet ports were designed to lay underneath the slice which were connected to channels to deliver oxygenated vs. deoxygenated media. Outlet ports were designed in an oval shape where deoxygenated media was delivered to the center of the slice and oxygenated media is delivered to the outer portion of the slice to mimic the location of oxygen across the intestine. An oxygen sensitive fluorescent dye, tris(2,2'-bipyridyl)dichlororuthenium(II), was used to characterize the tunability of the gradient. Viability of the tissue was confirmed by both fluorescence microscopy and FSCV. Additionally, we measured simultaneous serotonin and melatonin signaling with FSCV in the intestine for the first time. Overall, this chip provides a significant advance in our ability to culture intestinal slices ex vivo with the added benefit of direct access for measurements and imaging.

RevDate: 2024-02-20
CmpDate: 2024-02-20

Bass K, Sivaprakasam S, Dharmalingam-Nandagopal G, et al (2024)

Colonic ketogenesis, a microbiota-regulated process, contributes to blood ketones and protects against colitis in mice.

The Biochemical journal, 481(4):295-312.

Ketogenesis is considered to occur primarily in liver to generate ketones as an alternative energy source for non-hepatic tissues when glucose availability/utilization is impaired. 3-Hydroxy-3-methylglutaryl-CoA synthase-2 (HMGCS2) mediates the rate-limiting step in this mitochondrial pathway. Publicly available databases show marked down-regulation of HMGCS2 in colonic tissues in Crohn's disease and ulcerative colitis. This led us to investigate the expression and function of this pathway in colon and its relevance to colonic inflammation in mice. Hmgcs2 is expressed in cecum and colon. As global deletion of Hmgcs2 showed significant postnatal mortality, we used a conditional knockout mouse with enzyme deletion restricted to intestinal tract. These mice had no postnatal mortality. Fasting blood ketones were lower in these mice, indicating contribution of colonic ketogenesis to circulating ketones. There was also evidence of gut barrier breakdown and increased susceptibility to experimental colitis with associated elevated levels of IL-6, IL-1β, and TNF-α in circulation. Interestingly, many of these phenomena were mostly evident in male mice. Hmgcs2 expression in colon is controlled by colonic microbiota as evidenced from decreased expression in germ-free mice and antibiotic-treated conventional mice and from increased expression in a human colonic epithelial cell line upon treatment with aqueous extracts of cecal contents. Transcriptomic analysis of colonic epithelia from control mice and Hmgcs2-null mice indicated an essential role for colonic ketogenesis in the maintenance of optimal mitochondrial function, cholesterol homeostasis, and cell-cell tight-junction organization. These findings demonstrate a sex-dependent obligatory role for ketogenesis in protection against colonic inflammation in mice.

RevDate: 2024-02-19

Busch CBE, Bergman J, Nieuwdorp M, et al (2024)

Role of the intestine and its gut microbiota in metabolic syndrome and obesity.

The American journal of gastroenterology pii:00000434-990000000-01044 [Epub ahead of print].

The metabolic syndrome (MetSyn) is currently one of the biggest global health challenges, due to its impact on public health. MetSyn includes the cluster of metabolic disorders including obesity, high blood pressure, hyperglycemia, high triglyceride levels, and hepatic steatosis. Together these abnormalities increase the cardiovascular risk for individuals and pose a threat for healthcare systems worldwide. To better understand and address this complex issue, recent research has been increasingly focusing on unraveling the delicate interplay between metabolic disorders and the intestines, and more specifically our gut microbiome. The gut microbiome entails all microorganisms inhabiting the gastrointestinal tract and plays a pivotal role in metabolic processes and overall health of its host. Emerging evidence proves an association between the gut microbiome composition and aspects of MetSyn, such as obesity. Understanding these relationships is crucial as they offer valuable insights into the mechanisms underlying development and progression of metabolic disorders and possible treatment options. Yet how should we interpret this relationship? This review focuses on the interplay between the gut and MetSyn. In addition, we have reviewed the existing evidence of the gut microbiome and its association with and impact on metabolic disorders, in an attempt to understand the complex interactions and nature of this association. We also explored potential therapeutic options targeting the gut to modify metabolic disorders and obesity.

RevDate: 2024-02-19

Wijesekara T, Luo J, B Xu (2024)

Critical review on anti-inflammation effects of saponins and their molecular mechanisms.

Phytotherapy research : PTR [Epub ahead of print].

This review highlights the increasing interest in one of the natural compounds called saponins, for their potential therapeutic applications in addressing inflammation which is a key factor in various chronic diseases. It delves into the molecular mechanisms responsible for the anti-inflammatory effects of these amphiphilic compounds, prevalent in plant-based foods and marine organisms. Their structures vary with soap-like properties influencing historical uses in traditional medicine and sparking renewed scientific interest. Recent research focuses on their potential in chronic inflammatory diseases, unveiling molecular actions such as NF-κB and MAPK pathway regulation and COX/LOX enzyme inhibition. Saponin-containing sources like Panax ginseng and soybeans suggest novel anti-inflammatory therapies. The review explores their emerging role in shaping the gut microbiome, influencing composition and activity, and contributing to anti-inflammatory effects. Specific examples, such as Panax notoginseng and Gynostemma pentaphyllum, illustrate the intricate relationship between saponins, the gut microbiome, and their collective impact on immune regulation and metabolic health. Despite promising findings, the review emphasizes the need for further research to comprehend the mechanisms behind anti-inflammatory effects and their interactions with the gut microbiome, underscoring the crucial role of a balanced gut microbiome for optimal health and positioning saponins as potential dietary interventions for managing chronic inflammatory conditions.

RevDate: 2024-02-20

Wang X, Wang C, Liu K, et al (2024)

Association between sleep-related phenotypes and gut microbiota: a two-sample bidirectional Mendelian randomization study.

Frontiers in microbiology, 15:1341643.

BACKGROUND: An increasing body of evidence suggests a profound interrelation between the microbiome and sleep-related concerns. Nevertheless, current observational studies can merely establish their correlation, leaving causality unexplored.

STUDY OBJECTIVES: To ascertain whether specific gut microbiota are causally linked to seven sleep-related characteristics and propose potential strategies for insomnia prevention.

METHODS: The study employed an extensive dataset of gut microbiota genetic variations from the MiBioGen alliance, encompassing 18,340 individuals. Taxonomic classification was conducted, identifying 131 genera and 196 bacterial taxa for analysis. Sleep-related phenotype (SRP) data were sourced from the IEU OpenGWAS project, covering traits such as insomnia, chronotype, and snoring. Instrumental variables (IVs) were selected based on specific criteria, including locus-wide significance, linkage disequilibrium calculations, and allele frequency thresholds. Statistical methods were employed to explore causal relationships, including inverse variance weighted (IVW), MR-Egger, weighted median, and weighted Mode. Sensitivity analyses, pleiotropy assessments, and Bonferroni corrections ensured result validity. Reverse causality analysis and adherence to STROBE-MR guidelines were conducted to bolster the study's rigor.

RESULTS: Bidirectional Mendelian randomization (MR) analysis reveals a causative interplay between selected gut microbiota and sleep-related phenotypes. Notably, outcomes from the rigorously Bonferroni-corrected examination illuminate profound correlations amid precise compositions of the intestinal microbiome and slumber-associated parameters. Elevated abundance within the taxonomic ranks of class Negativicutes and order Selenomonadales was markedly associated with heightened susceptibility to severe insomnia (OR = 1.03, 95% CI: 1.02-1.05, p = 0.0001). Conversely, the augmented representation of the phylum Lentisphaerae stands in concord with protracted sleep duration (OR = 1.02, 95% CI: 1.01-1.04, p = 0.0005). Furthermore, heightened exposure to the genus Senegalimassilia exhibits the potential to ameliorate the manifestation of snoring symptoms (OR = 0.98, 95% CI: 0.96-0.99, p = 0.0001).

CONCLUSION: This study has unveiled the causal relationship between gut microbiota and SRPs, bestowing significant latent value upon future endeavors in both foundational research and clinical therapy.

RevDate: 2024-02-20

Yang MQ, Wang ZJ, Zhai CB, et al (2024)

Research progress on the application of 16S rRNA gene sequencing and machine learning in forensic microbiome individual identification.

Frontiers in microbiology, 15:1360457.

Forensic microbiome research is a field with a wide range of applications and a number of protocols have been developed for its use in this area of research. As individuals host radically different microbiota, the human microbiome is expected to become a new biomarker for forensic identification. To achieve an effective use of this procedure an understanding of factors which can alter the human microbiome and determinations of stable and changing elements will be critical in selecting appropriate targets for investigation. The 16S rRNA gene, which is notable for its conservation and specificity, represents a potentially ideal marker for forensic microbiome identification. Gene sequencing involving 16S rRNA is currently the method of choice for use in investigating microbiomes. While the sequencing involved with microbiome determinations can generate large multi-dimensional datasets that can be difficult to analyze and interpret, machine learning methods can be useful in surmounting this analytical challenge. In this review, we describe the research methods and related sequencing technologies currently available for application of 16S rRNA gene sequencing and machine learning in the field of forensic identification. In addition, we assess the potential value of 16S rRNA and machine learning in forensic microbiome science.

RevDate: 2024-02-20

Verma B, J Parkinson (2024)

HiTaxon: a hierarchical ensemble framework for taxonomic classification of short reads.

Bioinformatics advances, 4(1):vbae016.

MOTIVATION: Whole microbiome DNA and RNA sequencing (metagenomics and metatranscriptomics) are pivotal to determining the functional roles of microbial communities. A key challenge in analyzing these complex datasets, typically composed of tens of millions of short reads, is accurately classifying reads to their taxa of origin. While still performing worse relative to reference-based short-read tools in species classification, ML algorithms have shown promising results in taxonomic classification at higher ranks. A recent approach exploited to enhance the performance of ML tools, which can be translated to reference-dependent classifiers, has been to integrate the hierarchical structure of taxonomy within the tool's predictive algorithm.

RESULTS: Here, we introduce HiTaxon, an end-to-end hierarchical ensemble framework for taxonomic classification. HiTaxon facilitates data collection and processing, reference database construction and optional training of ML models to streamline ensemble creation. We show that databases created by HiTaxon improve the species-level performance of reference-dependent classifiers, while reducing their computational overhead. In addition, through exploring hierarchical methods for HiTaxon, we highlight that our custom approach to hierarchical ensembling improves species-level classification relative to traditional strategies. Finally, we demonstrate the improved performance of our hierarchical ensembles over current state-of-the-art classifiers in species classification using datasets comprised of either simulated or experimentally derived reads.

HiTaxon is available at:

RevDate: 2024-02-20

Wang Q, Fan X, Wu S, et al (2024)

PM-CNN: microbiome status recognition and disease detection model based on phylogeny and multi-path neural network.

Bioinformatics advances, 4(1):vbae013.

MOTIVATION: The human microbiome, found throughout various body parts, plays a crucial role in health dynamics and disease development. Recent research has highlighted microbiome disparities between patients with different diseases and healthy individuals, suggesting the microbiome's potential in recognizing health states. Traditionally, microbiome-based status classification relies on pre-trained machine learning (ML) models. However, most ML methods overlook microbial relationships, limiting model performance.

RESULTS: To address this gap, we propose PM-CNN (Phylogenetic Multi-path Convolutional Neural Network), a novel phylogeny-based neural network model for multi-status classification and disease detection using microbiome data. PM-CNN organizes microbes based on their phylogenetic relationships and extracts features using a multi-path convolutional neural network. An ensemble learning method then fuses these features to make accurate classification decisions. We applied PM-CNN to human microbiome data for status and disease detection, demonstrating its significant superiority over existing ML models. These results provide a robust foundation for microbiome-based state recognition and disease prediction in future research and applications.

PM-CNN software is available at

RevDate: 2024-02-20
CmpDate: 2024-02-20

Gregorczyk-Maga I, Kania M, Dąbrowska M, et al (2023)

The interplay between gingival crevicular fluid microbiome and metabolomic profile in intensively treated people with type 1 diabetes - a combined metagenomic/metabolomic approach cross-sectional study.

Frontiers in endocrinology, 14:1332406.

AIMS: This study aimed to assess the gingival crevicular fluid (GCF) microbiome and metabolome of adults with type 1 diabetes (T1D) treated with continuous subcutaneous insulin infusion (CSII).

METHODS: In this cross-sectional study, the GCF of adults with T1D treated with CSII and non-diabetic controls were sampled, and metagenomic/metabolomic analyses were performed.

RESULTS: In total, 65 participants with T1D and 45 healthy controls with a mean age of 27.05 ± 5.95 years were investigated. There were 22 cases of mild gingivitis (G) in the T1D group. There were no differences considering the Shannon and Chao indices and β-diversity between people with T1D and G, with T1D without G, and healthy controls. Differential taxa were identified, which were mainly enriched in people with T1D and G. Acetic acid concentration was higher in people with T1D, regardless of the presence of G, than in healthy controls. Propionic acid was higher in people with T1D and G than in healthy controls. Isobutyric and isovaleric acid levels were higher in individuals with T1D and G than in the other two subgroups. The concentration of valeric acid was lower and that of caproic acid was higher in people with T1D (regardless of gingival status) than in healthy controls.

CONCLUSIONS: The identification of early changes in periodontal tissues by targeting the microbiome and metabolome could potentially enable effective prevention and initial treatment of periodontal disease in people with T1D.

RevDate: 2024-02-20

Drechsler Y, Dong C, Clark DE, et al (2024)

Canine Atopic Dermatitis: Prevalence, Impact, and Management Strategies.

Veterinary medicine (Auckland, N.Z.), 15:15-29.

Atopic dermatitis (AD) is a common inflammatory and pruritic allergic skin disease in humans and dogs worldwide. The pathogenesis of AD is multifactorial, immunologically complex, and may involve genetic factors, epidermal barrier dysfunction, microbiome changes, immune dysregulation, and allergic sensitization. Across species, prevalence of AD is on the rise. At present, there is no cure for canine AD (CAD). The treatment for CAD is multifaceted and aimed at controlling the pruritus, associated inflammation, and infections, repairing the skin barrier function, and dietary management. This review presents data on prevalence, impact, and complex immunological interactions in AD with a focus on subsequent management of the disease in the canine population. A multimodal approach for management of CAD to address varying clinical signs and responses to therapies is discussed.

RevDate: 2024-02-20

Chuang PS, Yu SP, Liu PY, et al (2024)

A gauge of coral physiology: re-examining temporal changes in Endozoicomonas abundance correlated with natural coral bleaching.

ISME communications, 4(1):ycae001.

Bacteria contribute to many physiological functions of coral holobionts, including responses to bleaching. The bacterial genus, Endozoicomonas, dominates the microbial flora of many coral species and its abundance appears to be correlated with coral bleaching. However, evidences for decoupling of bleaching and Endozoicomonas abundance changes have also been reported. In 2020, a severe bleaching event was recorded at reefs in Taiwan, providing a unique opportunity to re-examine bleaching-Endozoicomonas association using multiple stony corals in natural environments. In this study, we monitored tissue color and microbiome changes in three coral species (Montipora sp., Porites sp., and Stylophora pistillata) in Kenting National Park, following the bleaching event. All tagged Montipora sp. and Porites sp. recovered from bleaching within 1 year, while high mortality occurred in S. pistillata. Microbiome analysis found no correlation of Endozoicomonas relative abundance and bleaching severity during the sampling period, but found a stronger correlation when the month in which bleaching occurred was excluded. Moreover, Endozoicomonas abundance increased during recovery months in Montipora sp. and Porites sp., whereas in S. pistillata it was nearly depleted. These results suggest that Endozoicomonas abundance may represent a gauge of coral health and reflect recovery of some corals from stress. Interestingly, even though different Endozoicomonas strains predominated in the three corals, these Endozoicomonas strains were also shared among coral taxa. Meanwhile, several Endozoicomonas strains showed secondary emergence during coral recovery, suggesting possible symbiont switching in Endozoicomonas. These findings indicate that it may be possible to introduce Endozoicomonas to non-native coral hosts as a coral probiotic.

RevDate: 2024-02-20
CmpDate: 2024-02-20

Cheng J, Zhou L, H Wang (2024)

Symbiotic microbial communities in various locations of the lung cancer respiratory tract along with potential host immunological processes affected.

Frontiers in cellular and infection microbiology, 14:1296295.

Lung cancer has the highest mortality rate among all cancers worldwide. The 5-year overall survival rate for non-small cell lung cancer (NSCLC) is estimated at around 26%, whereas for small cell lung cancer (SCLC), the survival rate is only approximately 7%. This disease places a significant financial and psychological burden on individuals worldwide. The symbiotic microbiota in the human body has been significantly associated with the occurrence, progression, and prognosis of various diseases, such as asthma, chronic obstructive pulmonary disease (COPD), and cystic fibrosis. Studies have demonstrated that respiratory symbiotic microorganisms and their metabolites play a crucial role in modulating immune function and contributing to the pathophysiology of lung cancer through their interactions with the host. In this review, we provide a comprehensive overview of the microbial characteristics associated with lung cancer, with a focus on the respiratory tract microbiota from different locations, including saliva, sputum, bronchoalveolar lavage fluid (BALF), bronchial brush samples, and tissue. We describe the respiratory tract microbiota's biodiversity characteristics by anatomical region, elucidating distinct pathological features, staging, metastasis, host chromosomal mutations, immune therapies, and the differentiated symbiotic microbiota under the influence of environmental factors. Our exploration investigates the intrinsic mechanisms linking the microbiota and its host. Furthermore, we have also provided a comprehensive review of the immune mechanisms by which microbiota are implicated in the development of lung cancer. Dysbiosis of the respiratory microbiota can promote or inhibit tumor progression through various mechanisms, including DNA damage and genomic instability, activation and regulation of the innate and adaptive immune systems, and stimulation of epithelial cells leading to the upregulation of carcinogenesis-related pathways.

RevDate: 2024-02-19

McMillan AS, Zhang G, Dougherty MK, et al (2024)

Metagenomic, metabolomic, and lipidomic shifts associated with fecal microbiota transplantation for recurrent Clostridioides difficile infection.

bioRxiv : the preprint server for biology pii:2024.02.07.579219.

Recurrent C. difficile infection (rCDI) is an urgent public health threat for which the last resort and lifesaving treatment is a fecal microbiota transplant (FMT). However, the exact mechanisms which mediate a successful FMT are not well understood. Here we use longitudinal stool samples collected from patients undergoing FMT to evaluate changes in the microbiome, metabolome, and lipidome after successful FMTs. We show changes in the abundance of many lipids, specifically acylcarnitines and bile acids, in response to FMT. These changes correlate with Enterobacteriaceae, which encode carnitine metabolism genes, and Lachnospiraceae, which encode bile salt hydrolases and baiA genes. LC-IMS-MS revealed a shift from microbial conjugation of primary bile acids pre-FMT to secondary bile acids post-FMT. Here we define the structural and functional changes in successful FMTs. This information will help guide targeted Live Biotherapeutic Product development for the treatment of rCDI and other intestinal diseases.

RevDate: 2024-02-19

Zaparte A, Dore E, White S, et al (2024)

Standard rodent diets differentially impact alcohol consumption and preference and gut microbiome diversity.

bioRxiv : the preprint server for biology pii:2024.02.06.579237.

Alcohol Use Disorder (AUD) is a complex and widespread disease with limited pharmacotherapies. Preclinical animal models of AUD use a variety of voluntary alcohol consumption procedures to recapitulate different phases of AUD including binge alcohol consumption and dependence. However, voluntary alcohol consumption in mice is widely variable rendering it difficult to reproduce results across labs. Accumulating evidence indicates that different brands of commercially available rodent chow can profoundly influence alcohol intake. In this study, we investigated the effects of three commercially available and widely used rodent diet formulations on alcohol consumption and preference in C57BL/6J mice using the 24h intermittent access procedure. The three brands of chow tested were LabDiet 5001 (LD 5001), LabDiet 5053 (LD 5053), and Teklad 2019S (TL2019S) from two companies (Research Diets and Envigo respectively). Mice fed LD5001 displayed the highest levels of alcohol consumption and preference followed by LD5053 and TL2019S. We also found that alcohol consumption and preference could be rapidly switched by changing the diet 48h prior to alcohol administration. Sucrose, saccharin, and quinine preference were not altered suggesting that the diets did not alter taste perception. We also found that mice fed LD5001 displayed increased quinine-resistant alcohol intake compared to mice fed TL2019S, suggesting that diets could influence the development of "compulsive" like alcohol consumption. We profiled the gut microbiome of water and alcohol drinking mice that were maintained on different diets and found significant differences in bacterial alpha and beta diversity, which could impact gut-brain axis signaling and alcohol consumption.

RevDate: 2024-02-19

Elmassry MM, Sugihara K, Chankhamjon P, et al (2024)

A meta-analysis of the gut microbiome in inflammatory bowel disease patients identifies disease-associated small molecules.

bioRxiv : the preprint server for biology pii:2024.02.07.579278.

Changes in the gut microbiome have been associated with several human diseases, but the molecular and functional details underlying these associations remain largely unknown. Here, we performed a multi-cohort analysis of small molecule biosynthetic gene clusters (BGCs) in 5,306 metagenomic samples of the gut microbiome from 2,033 Inflammatory Bowel Disease (IBD) patients and 833 matched healthy subjects and identified a group of Clostridia-derived BGCs that are significantly associated with IBD. Using synthetic biology, we discovered and solved the structures of six fatty acid amides as the products of the IBD-enriched BGCs. Using two mouse models of colitis, we show that the discovered small molecules disrupt gut permeability and exacerbate inflammation in chemically and genetically susceptible mice. These findings suggest that microbiome-derived small molecules may play a role in the etiology of IBD and represent a generalizable approach for discovering molecular mediators of microbiome-host interactions in the context of microbiome-associated diseases.

RevDate: 2024-02-19

Garcia CR, Norfolk WA, Howard AK, et al (2024)

Long-term gut colonization with ESBL-producing Escherichia coli in participants without known risk factors from the southeastern United States.

medRxiv : the preprint server for health sciences pii:2024.02.03.24302254.

UNLABELLED: We evaluated gut carriage of extended spectrum beta lactamase producing Enterobacteriaceae (ESBL-E) in southeastern U.S. residents without recent in-patient healthcare exposure. Study enrollment was January 2021-February 2022 in Athens, Georgia, U.S. and included a diverse population of 505 adults plus 50 child participants (age 0-5). Based on culture-based screening of stool samples, 4.5% of 555 participants carried ESBL-Es. This is slightly higher than reported in studies conducted 2012-2015, which found carriage rates of 2.5-3.9% in healthy U.S. residents. All ESBL-E confirmed isolates (n=25) were identified as Escherichia coli . Isolates belonged to 11 sequence types, with 48% classified as ST131. Ninety six percent of ESBL-E isolates carried a bla CTX-M gene. Isolated ESBL-Es frequently carried virulence genes as well as multiple classes of antibiotic resistance genes. Long-term colonization was common, with 64% of ESBL-E positive participants testing positive when rescreened three months later. One participant yielded isolates belonging to two different E. coli sequence types that carried bla CTX-M-1 genes on near-identical plasmids, suggesting intra-gut plasmid transfer. Isolation of E. coli on media without antibiotics revealed that ESBL- E. coli typically made up a minor fraction of the overall gut E. coli population, although in some cases they were the dominant strain. ESBL-E carriage was not associated with a significantly different stool microbiome composition. However, some microbial taxa were differentially abundant in ESBL-E carriers. Together, these results suggest that a small subpopulation of US residents are long-term, asymptomatic carriers of ESBL-Es, and may serve as an important reservoir for community spread of these ESBL genes.

IMPORTANCE: Antibiotic resistant bacteria, especially Enterobacteriaceae carrying ESBLs, have become an increasing public health threat. Increasing numbers of community-associated infections (47% of ESBL-E infections in the U.S.) in participants without healthcare exposure is particularly concerning. This study found that 4.5% of a southeastern United States study population, without in-patient healthcare exposure, were asymptomatically colonized with ESBL-E, and 64% of ESBL-E positive participants were still positive when rescreened 3 months later. This suggests that the gut microbiome of healthy participants may represent an understudied community reservoir of ESBL genes and ESBL Escherichia coli in the U.S.

RevDate: 2024-02-20

Handajani YS, Turana Y, Hengky A, et al (2024)

Probiotics supplementation or probiotic-fortified products on sarcopenic indices in older adults: systematic review and meta-analysis from recent randomized controlled trials.

Frontiers in aging, 5:1307762.

Introduction: A noteworthy correlation was seen between changes in the gut microbiome and sarcopenia in older adults. Along with increasing research on probiotic supplementation for various medical problems, we aimed to obtain evidence and summarize the effect of probiotic supplementation on sarcopenic indices among older adults. Methods: We utilized PubMed, EBSCO, and Proquest, in addition to manual search using synonyms and variation for 'probiotic,' 'sarcopenia,' and 'older adults.' Randomized controlled trials investigated the utilization of probiotics or probiotic-containing products in older adults with sarcopenic indices including muscle mass and strength. The random-effects model was applied to the meta-analysis process. Results: Seven studies were obtained with 733 pooled older adults. Probiotic supplementation resulted in a significant increase of muscle mass with adjusted SMD (Standardized Mean Difference) of 0.962 (95% CI: 0.288 to 1.635, p = 0.049) using till and trim analysis and muscle strength with SMD of 1.037 (95% CI: 0.077 to 1.996, p = 0.03). However, both outcomes were associated with significantly high heterogeneity (I[2] = 89.5% and I[2] = 89.9%, respectively). Conclusion: When opposed to a placebo, the probiotic treatment improved the amount of muscle and its endurance based on recent evidence, however, further studies should be done with larger samples and targeted populations.

RevDate: 2024-02-20

Taherkhani H, KavianFar A, Aminnezhad S, et al (2024)

Deciphering the impact of microbial interactions on COPD exacerbation: An in-depth analysis of the lung microbiome.

Heliyon, 10(4):e24775.

In microbiome studies, the diversity and types of microbes have been extensively explored; however, the significance of microbial ecology is equally paramount. The comprehension of metabolic interactions among the wide array of microorganisms in the lung microbiota is indispensable for understanding chronic pulmonary disease and for the development of potent treatments. In this investigation, metabolic networks were simulated, and ecological theory was employed to assess the diagnosis of COPD, subsequently suggesting innovative treatment strategies for COPD exacerbation. Lung sputum 16S rRNA paired-end data from 112 COPD patients were utilized, and a supervised machine-learning algorithm was applied to identify taxa associated with sex and mortality. Subsequently, an OTU table with Greengenes 99 % dataset was generated. Finally, the interactions between bacterial species were analyzed using a simulated metabolic network. A total of 1781 OTUs and 1740 bacteria at the genus level were identified. We employed an additional dataset to validate our analyses. Notably, among the more abundant genera, Pseudomonas was detected in females, while Lactobacillus was detected in males. Additionally, a decrease in bacterial diversity was observed during COPD exacerbation, and mortality was associated with the high abundance of the Staphylococcus and Pseudomonas genera. Moreover, an increase in Proteobacteria abundance was observed during COPD exacerbations. In contrast, COPD patients exhibited decreased levels of Firmicutes and Bacteroidetes. Significant connections between microbial ecology and bacterial diversity in COPD patients were discovered, highlighting the critical role of microbial ecology in the understanding of COPD. Through the simulation of metabolic interactions among bacteria, the observed dysbiosis in COPD was elucidated. Furthermore, the prominence of anaerobic bacteria in COPD patients was revealed to be influenced by parasitic relationships. These findings have the potential to contribute to improved clinical management strategies for COPD patients.

RevDate: 2024-02-20
CmpDate: 2024-02-20

Chang X, Zhang Y, Chen X, et al (2024)

Gut microbiome and serum amino acid metabolome alterations in autism spectrum disorder.

Scientific reports, 14(1):4037.

Gut microbiota and their metabolic products might play important roles in regulating the pathogenesis of autism spectrum disorder (ASD). The purpose of this study was to characterize gut microbiota and serum amino acid metabolome profiles in children with ASD. A non-randomized controlled study was carried out to analyze the alterations in the intestinal microbiota and their metabolites in patients with ASD (n = 30) compared with neurotypical controls (NC) (n = 30) by metagenomic sequencing to define the gut microbiota community and liquid chromatography/mass spectrometry (LC/MS) analysis to characterize the metabolite profiles. Compared with children in the NC group, those in the ASD group showed lower richness, higher evenness, and an altered microbial community structure. At the class level, Deinococci and Holophagae were significantly lower in children with ASD compared with TD. At the phylum level, Deinococcus-Thermus was significantly lower in children with ASD compared with TD. In addition, the functional properties (such as galactose metabolism) displayed significant differences between the ASD and NC groups. Five dominant altered species were identified and analyzed (LDA score > 2.0, P < 0.05), including Subdoligranulum, Faecalibacterium_praushitzii, Faecalibacterium, Veillonellaceae, and Rumminococcaceae. The peptides/nickel transport system was the main metabolic pathway involved in the differential species in the ASD group. Decreased ornithine levels and elevated valine levels may increase the risk of ASD through a metabolic pathway known as the nickel transport system. The microbial metabolism in diverse environments was negatively correlated with phascolarctobacterium succinatutens. Our study provides novel insights into compositional and functional alterations in the gut microbiome and metabolite profiles in ASD and the underlying mechanisms between metabolite and ASD.

RevDate: 2024-02-20
CmpDate: 2024-02-20

Carvalho LRRA, Boeder AM, Shimari M, et al (2024)

Antibacterial mouthwash alters gut microbiome, reducing nutrient absorption and fat accumulation in Western diet-fed mice.

Scientific reports, 14(1):4025.

Prolonged use of antibacterial mouthwash is linked to an increased risk of systemic disease. We aimed to investigate if disturbing the oral microbiota would impact the lower gut microbiome with functional effects in diet-induced obesity. Mice were exposed to oral chlorhexidine and fed a Western diet (WD). Food intake and weight gain were monitored, and metabolic function, blood pressure, and microbiota were analyzed. Chlorhexidine reduced the number of viable bacteria in the mouth and lowered species richness in the gut but with proportional enrichment of some bacteria linked to metabolic pathways. In mice fed a Western diet, chlorhexidine reduced weight gain, body fat, steatosis, and plasma insulin without changing caloric intake, while increasing colon triglycerides and proteins, suggesting reduced absorption of these nutrients. The mechanisms behind these effects as well as the link between the oral microbiome and small intestinal function need to be pinpointed. While the short-term effects of chlorhexidine in this model appear beneficial, potential long-term disruptions in the oral and gut microbiota and possible malabsorption should be considered.

RevDate: 2024-02-18

Li TP, Wang CH, Xie JC, et al (2024)

Microbial changes and associated metabolic responses modify host plant adaptation in Stephanitis nashi.

Insect science [Epub ahead of print].

Symbiotic microorganisms are essential for the physiological processes of herbivorous pests, including the pear lace bug Stephanitis nashi, which is known for causing extensive damage to garden plants and fruit trees due to its exceptional adaptability to diverse host plants. However, the specific functional effects of the microbiome on the adaptation of S. nashi to its host plants remains unclear. Here, we identified significant microbial changes in S. nashi on 2 different host plants, crabapple and cherry blossom, characterized by the differences in fungal diversity as well as bacterial and fungal community structures, with abundant correlations between bacteria or fungi. Consistent with the microbiome changes, S. nashi that fed on cherry blossom demonstrated decreased metabolites and downregulated key metabolic pathways, such as the arginine and mitogen-activated protein kinase signaling pathway, which were crucial for host plant adaptation. Furthermore, correlation analysis unveiled numerous correlations between differential microorganisms and differential metabolites, which were influenced by the interactions between bacteria or fungi. These differential bacteria, fungi, and associated metabolites may modify the key metabolic pathways in S. nashi, aiding its adaptation to different host plants. These results provide valuable insights into the alteration in microbiome and function of S. nashi adapted to different host plants, contributing to a better understanding of pest invasion and dispersal from a microbial perspective.

RevDate: 2024-02-20
CmpDate: 2024-02-20

Zou S, Yang C, Zhang J, et al (2024)

Multi-omic profiling reveals associations between the gut microbiome, host genome and transcriptome in patients with colorectal cancer.

Journal of translational medicine, 22(1):175.

BACKGROUND: Colorectal cancer (CRC) is the leading cancer worldwide. Microbial agents have been considered to contribute to the pathogenesis of different disease. But the underlying relevance between CRC and microbiota remain unclear.

METHODS: We dissected the fecal microbiome structure and genomic and transcriptomic profiles of matched tumor and normal mucosa tissues from 41 CRC patients. Of which, the relationship between CRC-associated bacterial taxa and their significantly correlated somatic mutated gene was investigated by exome sequencing technology. Differentially expressed functional genes in CRC were clustered according to their correlation with differentially abundant species, following by annotation with DAVID. The composition of immune and stromal cell types was identified by XCELL.

RESULTS: We identified a set of 22 microbial gut species associated with CRC and estimate the relative abundance of KEGG ontology categories. Next, the interactions between CRC-related gut microbes and clinical phenotypes were evaluated. 4 significantly mutated gene: TP53, APC, KRAS, SMAD4 were pointed out and the associations with cancer related microbes were identified. Among them, Fusobacterium nucleatum positively corelated with different host metabolic pathways. Finally, we revealed that Fusobacterium nucleatum modified the tumor immune environment by TNFSF9 gene expression.

CONCLUSION: Collectively, our multi-omics data could help identify novel biomarkers to inform clinical decision-making in the detection and diagnosis of CRC.

RevDate: 2024-02-20
CmpDate: 2024-02-20

Palberg D, Kaszecki E, Dhanjal C, et al (2024)

Impact of glyphosate and glyphosate-based herbicides on phyllospheric Methylobacterium.

BMC plant biology, 24(1):119.

Symbiotic Methylobacterium comprise a significant portion of the phyllospheric microbiome, and are known to benefit host plant growth, development, and confer tolerance to stress factors. The near ubiquitous use of the broad-spectrum herbicide, glyphosate, in farming operations globally has necessitated a more expansive evaluation of the impacts of the agent itself and formulations containing glyphosate on important components of the plant phyllosphere, including Methylobacterium.This study provides an investigation of the sensitivity of 18 strains of Methylobacterium to glyphosate and two commercially available glyphosate-based herbicides (GBH). Nearly all strains of Methylobacterium showed signs of sensitivity to the popular GBH formulations WeatherMax® and Transorb® in a modified Kirby Bauer experiment. However, exposure to pure forms of glyphosate did not show a significant effect on growth for any strain in both the Kirby Bauer test and in liquid broth, until polysorbate-20 (Tween20) was added as a surfactant. Artificially increasing membrane permeability through the introduction of polysorbate-20 caused a 78-84% reduction in bacterial cell biomass relative to controls containing glyphosate or high levels of surfactant only (0-9% and 6-37% reduction respectively). Concentrations of glyphosate as low as 0.05% w/v (500 µg/L) from both commercial formulations tested, inhibited the culturability of Methylobacterium on fresh nutrient-rich medium.To better understand the compatibility of important phyllospheric bacteria with commercial glyphosate-based herbicides, this study endeavours to characterize sensitivity in multiple strains of Methylobacterium, and explore possible mechanisms by which toxicity may be induced.

RevDate: 2024-02-18

Liu J, Dai Q, Qu T, et al (2024)

Ameliorating effects of transcutaneous auricular vagus nerve stimulation on a mouse model of constipation-predominant irritable bowel syndrome.

Neurobiology of disease pii:S0969-9961(24)00039-1 [Epub ahead of print].

Limited treatment options have been shown to alter the natural course of constipation-predominant irritable bowel syndrome (IBS-C). Therefore, safer and more effective approaches are urgently needed. We investigated the effects of transcutaneous auricular vagus nerve stimulation (taVNS) in a mouse model of IBS-C. In the current study, C57BL/6 mice were randomly divided into normal control, IBS-C model control, sham-electrostimulation (sham-ES), taVNS, and drug treatment groups. The effects of taVNS on fecal pellet number, fecal water content, and gastrointestinal transit were evaluated in IBS-C model mice. We assessed the effect of taVNS on visceral hypersensitivity using the colorectal distention test. 16S rRNA sequencing was used to analyze the fecal microbiota of the experimental groups. First, we found that taVNS increased fecal pellet number, fecal water content, and gastrointestinal transit in IBS-C model mice compared with the sham-ES group. Second, taVNS significantly decreased the abdominal withdrawal reflex (AWR) score compared with the sham-ES group, thus relieving visceral hyperalgesia. Third, the gut microbiota outcomes showed that taVNS restored Lactobacillus abundance while increasing Bifidobacterium probiotic abundance at the genus level. Notably, taVNS increased the number of c-kit-positive interstitial cells of Cajal (ICC) in the myenteric plexus region in IBS-C mice compared with the sham-ES group. Therefore, our study indicated that taVNS effectively ameliorated IBS-C in the gut microbiota and ICC.

RevDate: 2024-02-18

Chen J, Cai Y, Wang Z, et al (2024)

Solid-state fermentation of corn straw using synthetic microbiome to produce fermented feed: The feed quality and conversion mechanism.

The Science of the total environment pii:S0048-9697(24)01173-2 [Epub ahead of print].

Straw is a typical biomass resource which can be converted into high nutritional value feed via microbial fermentation. The degradation and conversion of straw using a synthetic microbial community (SMC-8) was functionally investigated to characterise its nitrogen conversion and carbon metabolism. Four species of bacteria were found to utilise >20 % of the inorganic nitrogen within 15 h, and the ratio of the diameter of fungal transparent circles (D) to the diameter of the colony (d) of the four fungal species was >1. Solid-state fermentation of corn straw increased the total amino acid (AA) content by 41.69 %. The absolute digestibility of fermented corn straw dry weight (DW) and true protein was 34.34 % and 45.29 %, respectively. Comprehensive analysis of functional proteins revealed that Aspergillus niger, Trichoderma viride, Cladosporium cladosporioides, Bacillus subtilis and Acinetobacter johnsonii produce a complex enzyme system during corn straw fermentation, which plays a key role in the degradation of lignocellulose. This study provided a new insight in utilizing corn straw.

RevDate: 2024-02-18

Singh JP, Bottos EM, Van Hamme JD, et al (2024)

Microbial composition and function in reclaimed mine sites along a reclamation chronosequence become increasingly similar to undisturbed reference sites.

The Science of the total environment pii:S0048-9697(24)01135-5 [Epub ahead of print].

Mine reclamation historically focuses on enhancing plant coverage to improve below and aboveground ecology. However, there is a great need to study the role of soil microorganisms in mine reclamation, particularly long-term studies that track the succession of microbial communities. Here, we investigate the trajectory of microbial communities of mining sites reclaimed between three and 26 years. We used high-throughput amplicon sequencing to characterize the bacterial and fungal communities. We quantified how similar the reclaimed sites were to unmined, undisturbed reference sites and explored the trajectory of microbial communities along the reclamation chronosequence. We also examined the ecological processes that shape the assembly of bacterial communities. Finally, we investigated the functional potential of the microbial communities through metagenomic sequencing. Our results reveal that the reclamation age significantly impacted the community compositions of bacterial and fungal communities. As the reclamation age increases, bacterial and fungal communities become similar to the unmined, undisturbed reference site, suggesting a favorable succession in microbial communities. The bacterial community assembly was also significantly impacted by reclamation age and was primarily driven by stochastic processes, indicating a lesser influence of environmental properties on the bacterial community. Furthermore, our read-based metagenomic analysis showed that the microbial communities' functional potential increasingly became similar to the reference sites. Additionally, we found that the plant richness increased with the reclamation age. Overall, our study shows that both above- and belowground ecological properties of reclaimed mine sites trend towards undisturbed sites with increasing reclamation age. Further, it demonstrates the importance of microbial genomics in tracking the trajectory of ecosystem reclamation.

RevDate: 2024-02-18

Jiang Q, Sherlock DN, Elolimy AA, et al (2024)

Feeding a Saccharomyces cerevisiae fermentation product during a gut barrier challenge in lactating Holstein cows impacts the ruminal microbiota and metabolome.

Journal of dairy science pii:S0022-0302(24)00489-2 [Epub ahead of print].

Through its influence on the gut microbiota, feeding of Saccharomyces cerevisiae fermentation products (SCFP) has been a successful strategy to enhance the health of dairy cows during periods of physiological stresses. Although production and metabolic outcomes from feeding SCFP are well-known, combined impacts on the ruminal microbiota and metabolome during gut barrier challenges remain unclear. To address this gap in knowledge, multiparous Holstein cows (97.1 ± 7.6 DIM; n = 8/group) fed a control diet (CON) or CON plus 19 g/d SCFP for 9 wk were subjected to a feed restriction (FR) challenge for 5 d, during which they were fed 40% of their ad-libitum intake from the 7 d before FR. DNA extracted from ruminal fluid was subjected to PacBio Full-Length 16S rRNA gene sequencing, RT-PCR of 12 major ruminal bacteria, and metabolomics analysis of up to 189 metabolites via GC-MS. High-quality amplicon sequence analyses were performed with Targeted Amplicon Diversity Analysis (TADA), MicrobiomeAnalyst, PICRUSt2, and STAMP software, while metabolomics data were analyzed via MetaboAnalyst 5.0. Ruminal fluid metabolites from the SCFP group exhibited a greater α diversity Chao 1 (P = 0.03) and Shannon indices (P = 0.05), and the PLS-DA analysis clearly discriminated metabolite profiles between dietary groups. The abundance of CPla_4_termite_group, Candidatus_Saccharimonas, Oribacterium, and Pirellula genus in cows fed SCFP was greater. In the SCFP group, concentrations of ethanolamine, 2-amino-4,6-dihydroxypyrimidine, glyoxylic acid, serine, threonine, cytosine, stearic acid, and pyrrole-2-carboxylic acid were greater in ruminal fluid. Both Fretibacterium and Succinivibrio abundance were positively correlated with metabolites across various biological processes: gamma-aminobutyric acid, galactose, butane-2,3-diol, fructose, 5-amino pentanoic acid, β-aminoisobutyric acid, ornithine, malonic acid, 3-hydroxy-3-methylbutyric acid, hexanoic acid, heptanoic acid, cadaverine, glycolic acid, β-alanine, 2-hydroxybutyric acid, methyl alanine, and alanine. In the SCFP group, compared with CON, the mean proportion of 14 predicted pathways based on metabolomics data was greater, while 10 predicted pathways were lower. Integrating metabolites and upregulated predicted enzymes (NADP+-dependent glucose-6-phosphate dehydrogenase, 6-phosphogluconate dehydrogenase, serine: glyoxylate aminotransferase, and D-glycerate 3-kinase) indicated that the pentose phosphate pathway and photorespiration pathway were most upregulated by SCFP. Overall, SCFP during FR led to alterations in ruminal microbiota composition and key metabolic pathways. Among those, there was a shift from the tricarboxylic acid (TCA) cycle to the glyoxylate cycle and nitrogenous base production was enhanced.

RevDate: 2024-02-18

Bashir B, Alam S, Khandale N, et al (2024)

Opening avenues for treatment of neurodegenerative disease using post-biotics: Breakthroughs and bottlenecks in clinical translation.

Ageing research reviews pii:S1568-1637(24)00054-0 [Epub ahead of print].

Recent studies have indicated the significant involvement of the gut microbiome in both human physiology and pathology. Additionally, therapeutic interventions based on microbiome approaches have been employed to enhance overall health and address various diseases including aging and neurodegenerative disease (ND). Researchers have explored potential links between these areas, investigating the potential pathogenic or therapeutic effects of intestinal microbiota in diseases. This article provides a summary of established interactions between the gut microbiome and ND. Post-biotic is believed to mediate its neuroprotection by elevating the level of dopamine and reducing the level of α-synuclein in substantia nigra, protecting the loss of dopaminergic neurons, reducing the aggregation of NFT, reducing the deposition of amyloid β peptide plagues and ameliorating motor deficits. Moreover, mediates its neuroprotective activity by inhibiting the inflammatory response (decreasing the expression of TNFα, iNOS expression, free radical formation, overexpression of HIF-1α), apoptosis (i.e. active caspase-3, TNF-α, maintains the level of Bax/Bcl-2 ratio) and promoting BDNF secretion. It is also reported to have good antioxidant activity. This review offers an overview of the latest findings from both preclinical and clinical trials concerning the use of post-biotics in ND.

RevDate: 2024-02-20
CmpDate: 2024-02-20

Hull A, Atilano ML, Gergi L, et al (2024)

Lysosomal storage, impaired autophagy and innate immunity in Gaucher and Parkinson's diseases: insights for drug discovery.

Philosophical transactions of the Royal Society of London. Series B, Biological sciences, 379(1899):20220381.

Impairment of autophagic-lysosomal pathways is increasingly being implicated in Parkinson's disease (PD). GBA1 mutations cause the lysosomal storage disorder Gaucher disease (GD) and are the commonest known genetic risk factor for PD. GBA1 mutations have been shown to cause autophagic-lysosomal impairment. Defective autophagic degradation of unwanted cellular constituents is associated with several pathologies, including loss of normal protein homeostasis, particularly of α-synuclein, and innate immune dysfunction. The latter is observed both peripherally and centrally in PD and GD. Here, we will discuss the mechanistic links between autophagy and immune dysregulation, and the possible role of these pathologies in communication between the gut and brain in these disorders. Recent work in a fly model of neuronopathic GD (nGD) revealed intestinal autophagic defects leading to gastrointestinal dysfunction and immune activation. Rapamycin treatment partially reversed the autophagic block and reduced immune activity, in association with increased survival and improved locomotor performance. Alterations in the gut microbiome are a critical driver of neuroinflammation, and studies have revealed that eradication of the microbiome in nGD fly and mouse models of PD ameliorate brain inflammation. Following these observations, lysosomal-autophagic pathways, innate immune signalling and microbiome dysbiosis are discussed as potential therapeutic targets in PD and GD. This article is part of a discussion meeting issue 'Understanding the endo-lysosomal network in neurodegeneration'.

RevDate: 2024-02-18

Pyle HJ, Evans JC, Artami M, et al (2024)

Assessment of the Cutaneous Hormone Landscapes and Microbiomes in Vulvar Lichen Sclerosus.

The Journal of investigative dermatology pii:S0022-202X(24)00111-8 [Epub ahead of print].

Vulvar lichen sclerosus (VLS) is a progressive skin disease of unknown etiology. In this longitudinal case-control exploratory study, we evaluated the hormonal and microbial landscapes in 18 postmenopausal women (mean [SD] age: 64.4 [8.4]) with vulvar lichen sclerosus and controls. We reevaluated the VLS patients after 10-14 weeks of daily topical Class I steroid. We found that groin cutaneous estrone was lower in vulvar lichen sclerosus versus controls (-22.33, 95% CI -36.96 to -7.70; P = 0.006); cutaneous progesterone was higher (5.73, 95% CI 3.74 to 7.73; P< 0.0001). Forehead 11-deoxycortisol (-0.24, 95% CI -0.42 to -0.06; P = 0.01) and testosterone (-7.22, 95% CI -12.83 to -1.62; P = 0.02) were lower in disease. With treatment, cutaneous estrone (-7.88, 95% CI -44.07 to 28.31; P = 0.62), progesterone (2.02, 95% CI -2.08 to 6.11; P = 0.29), and 11-deoxycortisol (-0.13, 95% CI -0.32 to 0.05; P = 0.15) normalized; testosterone remained suppressed (-7.41, 95% CI -13.38 to -1.43; P = 0.02). 16S rRNA V1-V3 and ITS1 amplicon sequencing revealed bacterial and fungal microbiome alterations in disease. Findings suggest that cutaneous sex hormone and bacterial microbiome alterations may be associated with VLS in postmenopausal women.

RevDate: 2024-02-18

Mei S, Wang X, Lei F, et al (2024)

Focus on studying the effects of different exposure durations on the microbial structures and characteristics of three types of body fluids.

Forensic science international, 356:111949 pii:S0379-0738(24)00030-6 [Epub ahead of print].

BACKGROUND: Body fluid traceability inferences can provide important clues to the investigation of forensic cases. Microbiome has been proven to be well applied in forensic body fluid traceability studies. Most of the specimens at crime scenes are often exposed to the external environment when collected, so it is extremely important to exploring the structure characteristics of microbial communities of body fluid samples under different exposure durations for tracing the origin of body fluids based on microorganisms.

METHODS: Full-length 16S rRNA sequencing technology and multiple data analysis methods were used to explore the microbial changes in three types of body fluid samples at five different exposure time points.

RESULTS: With increasing exposure time, the Proteobacteria abundance gradually increased in the negative control and body fluid samples, and the Bacteroidetes and Firmicutes abundance decreased gradually, but the relative abundance of dominant genera in each body fluid remained dynamically stable. The microbial community structures of those samples from the same individual at different exposure durations were similar, and there were no significant differences in the microbial community structures among the different exposure time points. LEfSe and random forest analyses were applied to screen stable and differential microbial markers among body fluids, such as Streptococcus thermophilus, Streptococcus pneumoniae and Haemophilus parainfluenzae in saliva; Lactobacillus iners and Streptococcus agalactiae in vaginal fluid.

CONCLUSIONS: There were no significant differences in microbial community structures of the three types of body fluid samples exposed to the environment for various time periods, although the relative abundance of some microbes in these samples would change. The exposed samples could still be traced back to their source of the body fluid samples using the microbial community structures.

RevDate: 2024-02-18

Deng C, Chen T, Qiu Z, et al (2024)

A mixed blessing of influent leachate microbes in downstream biotreatment systems of a full-scale landfill leachate treatment plant.

Water research, 253:121310 pii:S0043-1354(24)00212-4 [Epub ahead of print].

In landfill leachate treatment plants (LLTPs), the microbiome plays a pivotal role in the decomposition of organic compounds, reduction in nutrient levels, and elimination of toxins. However, the effects of microbes in landfill leachate influents on downstream treatment systems remain poorly understood. To address this knowledge gap, we collected 23 metagenomic and 12 metatranscriptomic samples from landfill leachate and activated sludge from various treatment units in a full-scale LLTP. We successfully recovered 1,152 non-redundant metagenome-assembled genomes (MAGs), encompassing a wide taxonomic range, including 48 phyla, 95 classes, 166 orders, 247 families, 238 genera, and 1,152 species. More diverse microbes were observed in the influent leachate than in the downstream biotreatment systems, among which, an unprecedented ∼30 % of microbes with transcriptional expression migrated from the influent to the biological treatment units. Network analysis revealed that 399 shared MAGs across the four units exhibited high node centrality and degree, thus supporting enhanced interactions and increased stability of microbial communities. Functional reconstruction and genome characterization of MAGs indicated that these shared MAGs possessed greater capabilities for carbon, nitrogen, sulfur, and arsenic metabolism compared to non-shared MAGs. We further identified a novel species of Zixibacteria in the leachate influent with discrete lineages from those in other environments that accounted for up to 17 % of the abundance of the shared microbial community and exhibited notable metabolic versatility. Meanwhile, we presented groundbreaking evidence of the involvement of Zixibacteria-encoded genes in the production of harmful gas emissions, such as N2O and H2S, at the transcriptional level, thus suggesting that influent microbes may pose safety risks to downstream treatment systems. In summary, this study revealed the complex impact of the influent microbiome on LLTP and emphasizes the need to consider these microbial characteristics when designing treatment technologies and strategies for landfill leachate management.

RevDate: 2024-02-19
CmpDate: 2024-02-19

Xu C, Hao M, Zai X, et al (2024)

A new perspective on gut-lung axis affected through resident microbiome and their implications on immune response in respiratory diseases.

Archives of microbiology, 206(3):107.

The highly diverse microbial ecosystem of the human body colonizes the gastrointestinal tract has a profound impact on the host's immune, metabolic, endocrine, and other physiological processes, which are all interconnected. Specifically, gut microbiota has been found to play a crucial role in facilitating the adaptation and initiation of immune regulatory response through the gastrointestinal tract affecting the other distal mucosal sites such as lungs. A tightly regulated lung-gut axis during respiratory ailments may influence the various molecular patterns that instructs priming the disease severity to dysregulate the normal function. This review provides a comprehensive summary of current research on gut microbiota dysbiosis in respiratory diseases including asthma, pneumonia, bronchopneumonia, COPD during infections and cancer. A complex-interaction among gut microbiome, associated metabolites, cytokines, and chemokines regulates the protective immune response activating the mucosal humoral and cellular response. This potential mechanism bridges the regulation patterns through the gut-lung axis. This paper aims to advance the understanding of the crosstalk of gut-lung microbiome during infection, could lead to strategize to modulate the gut microbiome as a treatment plan to improve bad prognosis in various respiratory diseases.

RevDate: 2024-02-20
CmpDate: 2024-02-19

García-Serquén AL, Chumbe-Nolasco LD, Navarrete AA, et al (2024)

Traditional potato tillage systems in the Peruvian Andes impact bacterial diversity, evenness, community composition, and functions in soil microbiomes.

Scientific reports, 14(1):3963.

The soil microbiome, a crucial component of agricultural ecosystems, plays a pivotal role in crop production and ecosystem functioning. However, its response to traditional tillage systems in potato cultivation in the Peruvian highlands is still far from understood. Here, ecological and functional aspects of the bacterial community were analyzed based on soil samples from two traditional tillage systems: 'chiwa' (minimal tillage) and 'barbecho' (full tillage), in the Huanuco region of the Peruvian central Andes. Similar soil bacterial community composition was shown for minimal tillage system, but it was heterogeneous for full tillage system. This soil bacterial community composition under full tillage system may be attributed to stochastic, and a more dynamic environment within this tillage system. 'Chiwa' and 'barbecho' soils harbored distinct bacterial genera into their communities, indicating their potential as bioindicators of traditional tillage effects. Functional analysis revealed common metabolic pathways in both tillage systems, with differences in anaerobic pathways in 'chiwa' and more diverse pathways in 'barbecho'. These findings open the possibilities to explore microbial bioindicators for minimal and full tillage systems, which are in relationship with healthy soil, and they can be used to propose adequate tillage systems for the sowing of potatoes in Peru.

RevDate: 2024-02-17

Robinson JM, Breed MF, R Beckett (2024)

Probiotic Cities: microbiome-integrated design for healthy urban ecosystems.

Trends in biotechnology pii:S0167-7799(24)00005-2 [Epub ahead of print].

Combining microbiome science and biointegrated design offers opportunities to help address the intertwined challenges of urban ecosystem degradation and human disease. Biointegrated materials have the potential to combat superbugs and remediate pollution while inoculating landscape materials with microbiota can promote human immunoregulation and biodiverse green infrastructure, contributing to 'probiotic cities'.

RevDate: 2024-02-17

Caviness PC, Lazarenko OP, Blackburn ML, et al (2024)

Phenolic acids prevent sex-steroid deficiency-induced bone loss and bone marrow adipogenesis in mice.

The Journal of nutritional biochemistry pii:S0955-2863(24)00034-2 [Epub ahead of print].

Phenolic acids, such as hippuric acid (HA) and 3-(3-hydroxyphenyl) propionic acid (3-3-PPA), can be produced from microbiome digestion of polyphenols. Previously it was found that HA and 3-3-PPA facilitate bone formation and suppress bone resorption. However, the mechanism of action by which HA and 3-3-PPA protect bone from degeneration is currently unknown. In this report, we present that HA and 3-3-PPA suppression of bone resorption is able to ameliorate bone loss in an ovariectomy (OVX) osteopenic mouse model though not to the extent of Zoledronic acid (ZA). HA and 3-3-PPA treatments were shown to significantly decrease bone marrow adipocyte-like cell formation and inhibited gene expression of key adipogenesis regulator peroxisome proliferator activated receptor gamma (PPARγ) and lipoprotein lipase (Lpl) in bone from OVX mice. In addition, ChIP experiments showed that the association between PPARγ and Lpl promoter region in pre-adipocyte-like cells was significantly suppressed following HA or 3-3-PPA treatment. Contrasting HA and 3-3-PPA, ZA significantly increased TRAP activity in the area close to growth plate and significantly suppressed bone cell proliferation. These data suggest that phenolics acids such as HA or 3-3-PPA may prevent bone degeneration after OVX through suppression of inflammatory milieu in the bone.

RevDate: 2024-02-17

Williams LM, S Cao (2024)

Harnessing and delivering microbial metabolites as therapeutics via advanced pharmaceutical approaches.

Pharmacology & therapeutics pii:S0163-7258(24)00025-1 [Epub ahead of print].

Microbial metabolites have emerged as key players in the interplay between diet, the gut microbiome, and host health. Two major classes, short-chain fatty acids (SCFAs) and tryptophan (Trp) metabolites, are recognized to regulate inflammatory, immune, and metabolic responses within the host. Given that many human diseases are associated with dysbiosis of the gut microbiome and consequent reductions in microbial metabolite production, the administration of these metabolites represents a direct, multi-targeted treatment. While a multitude of preclinical studies showcase the therapeutic potential of both SCFAs and Trp metabolites, they often rely on high doses and frequent dosing regimens to achieve systemic effects, thereby constraining their clinical applicability. To address these limitations, a variety of pharmaceutical formulations approaches that enable targeted, delayed, and/or sustained microbial metabolite delivery have been developed. These approaches, including enteric encapsulations, esterification to dietary fiber, prodrugs, and nanoformulations, pave the way for the next generation of microbial metabolite-based therapeutics. In this review, we first provide an overview of the roles of microbial metabolites in maintaining host homeostasis and outline how compromised metabolite production contributes to the pathogenesis of inflammatory, metabolic, autoimmune, allergic, infectious, and cancerous diseases. Additionally, we explore the therapeutic potential of metabolites in these disease contexts. Then, we provide a comprehensive and up-to-date review of the pharmaceutical strategies that have been employed to enhance the therapeutic efficacy of microbial metabolites, with a focus on SCFAs and Trp metabolites.

RevDate: 2024-02-17

Han A, Yang M, Chen B, et al (2024)

Microbiome and its relevance to indigenous inflammatory bowel diseases in China.

Gene pii:S0378-1119(24)00138-0 [Epub ahead of print].

BACKGROUND: Inflammatory Bowel Disease (IBD) is a chronic inflammatory disorder of the gastrointestinal tract with an unknown etiology. Although dysbiosis is implicated in its pathogenesis, deep sequencing and oral microbiota study in Chinese IBD patients is absent.

AIM: To explore the role of oral / intestinal microbiota in patients with IBD and the potential associations therein.

METHODS: Clinical data, fecal and saliva samples were harvested from 80 patients with IBD (Crohn's disease, CD, n = 69; Ulcerative colitis, UC, n = 11) and 24 normal controls. Microbiomics (16S rRNA sequencing and 16S rRNA full-length sequencing) were used to detect and analyze the difference between IBD patients and normal control.

RESULTS: Compared with normal controls, a higher abundance of the intestinal Shigella spp. (Shigella flexneri and Shigella sonnei, which were positively relate to the severity of IBD), lower abundance of intestinal probiotics (Prevotella, Faecalibacterium and Roseburia), and higher abundance of oral Neisseria were present in IBD patients with microbiome. The higher inflammation-related markers, impaired hepatic and renal function, and dyslipidaemia were present in patients with IBD. A higher intake of red meat and increased abundance of Clostridium in the gut were found in CD patients, while the elevated abundance of Ruminococcus in the gut was showed in UC ones. The bacterial composition of saliva and fecal samples was completely different, yet there was some correlation in the distribution of dominant probiotics.

CONCLUSION: Enteric dysbacteriosis and the infections of pathogenic bacteria (Shigella) may associate with the occurrence or development of IBD.

RevDate: 2024-02-17

Sun Y, X Fu (2024)

Comprehensive examination of travel-related antimicrobial resistance and the gut microbiome.

RevDate: 2024-02-17

Chen Q, Wu C, Xu J, et al (2024)

Donor-recipient intermicrobial interactions impact transfer of subspecies and fecal microbiota transplantation outcome.

Cell host & microbe pii:S1931-3128(24)00017-9 [Epub ahead of print].

Studies on fecal microbiota transplantation (FMT) have reported inconsistent connections between clinical outcomes and donor strain engraftment. Analyses of subspecies-level crosstalk and its influences on lineage transfer in metagenomic FMT datasets have proved challenging, as single-nucleotide polymorphisms (SNPs) are generally not linked and are often absent. Here, we utilized species genome bin (SGB), which employs co-abundance binning, to investigate subspecies-level microbiome dynamics in patients with autism spectrum disorder (ASD) who had gastrointestinal comorbidities and underwent encapsulated FMT (Chinese Clinical Trial: 2100043906). We found that interactions between donor and recipient microbes, which were overwhelmingly phylogenetically divergent, were important for subspecies transfer and positive clinical outcomes. Additionally, a donor-recipient SGB match was indicative of a high likelihood of strain transfer. Importantly, these ecodynamics were shared across FMT datasets encompassing multiple diseases. Collectively, these findings provide detailed insight into specific microbial interactions and dynamics that determine FMT success.

RevDate: 2024-02-17

Iordache A, Fuursted K, Rift CV, et al (2024)

Hepatic granulomas following liver transplantation: A retrospective survey, and analysis of possible microbiological etiology.

Pathology, research and practice, 255:155201 pii:S0344-0338(24)00112-2 [Epub ahead of print].

BACKGROUND: Liver granulomas have always been a diagnostic challenge for pathologists. They have been described in up to 15% of liver biopsies and can also be seen in liver allograft biopsy specimens, but there is a paucity of information regarding the prevalence and associated etiologic factors of granulomas in liver transplanted patients. The aim of this study is to shed light on the etiology of liver granulomas.

METHODS: Liver biopsies from liver transplanted patients, in the period from 01.01.2011 - 01.05.2017, were examined. We registered the histo-morphological characteristics and clinicopathological data of all biopsies and performed next-generation sequencing (NGS) to detect possible pathogens (bacteria, fungi, and parasites) in the biopsies containing granulomas.

RESULTS: We reviewed a total of 400 liver biopsies from 217 liver transplant patients. Of these, 131 liver biopsies (32.8%) from 98 patients (45.2%) revealed granulomas. Most were epithelioid granulomas located parenchymal and were detected in 115 (87.7%) biopsies. We also identified 10 cases (7.6%) with both lobular and portal granulomas and six biopsies (4.5%) with portal granulomas alone. In 54 biopsies (41.2%), granulomas were found in biopsies with acute cellular rejection (ACR). Fifty (51%) patients with granulomas underwent liver transplantation for autoimmune-related end-stage liver disease (AILD). The granulomas were found most frequently in the first six months after transplantation, where patients also more often were biopsied. NGS analysis did not reveal any potential infectious agent, and no significant differences were observed in the microbiological diversity (microbiome) between clinical- and granuloma characteristics concerning bacteria, fungi, and parasites.

CONCLUSION: Our study confirmed that granulomas are frequently seen in liver allograft biopsy specimens, and most often localized in the parenchyma, occurring in the first post-transplant period in patients with AILD, and often seen simultaneously with episodes of ACR. Neither a specific microbiological etiological agent nor a consistent microbiome was detected in any case.

RevDate: 2024-02-17

Majka Z, Zapala B, Krawczyk A, et al (2024)

Direct oral and fiber-derived butyrate supplementation as an anti-obesity treatment via different targets.

Clinical nutrition (Edinburgh, Scotland), 43(3):869-880 pii:S0261-5614(24)00051-7 [Epub ahead of print].

BACKGROUND & AIMS: Butyric (one of the short-chain fatty acids), a major byproduct of the fermentation of non-digestible carbohydrates (e.g. fiber), is supposed to have anti-obesity and anti-inflammatory properties. However, butyrate's potential and mechanism in preventing obesity and the efficient form of administration remain to be clarified.

METHODS: Hence, we studied the effect of oral supplementation with 5% (w/w) sodium butyrate and 4% (w/w) β-glucan (fiber) on young male mice (C57BL/6J) with high-fat diet-induced obesity (HFD: 60 kcal% of fat + 1% of cholesterol). Six weeks old mice were fed diets based on HFD or control (AIN-93G) diet with/without supplements for 4 weeks. The unique, interdisciplinary approach combining several Raman-based techniques (including Raman microscopy and fiber optic Raman spectroscopy) and next-generation sequencing was used to ex vivo analyze various depots of the adipose tissue (white, brown, perivascular) and gut microbiome, respectively.

RESULTS: The findings demonstrate that sodium butyrate more effectively prevent the pathological increase in body weight caused by elevated saturated fatty acids influx linked to a HFD in comparison to β-glucan, thereby entirely inhibiting diet-induced obesity. Moreover, butyrate significantly affects the white adipose tissue (WAT) reducing the epididymal WAT mass in comparison to HFD without supplements, and decreasing lipid saturation in the epididymal WAT and perivascular adipose tissue of the thoracic aorta. Contrarily, β-glucan significantly changes the composition and diversity of the gut microbiome, reversing the HFD effect, but shows no effect on the epididymal WAT mass and therefore the weight gain inhibition is not as effective as with sodium butyrate.

CONCLUSIONS: Here, oral supplementation with sodium butyrate and β-glucan (fiber) has been proven to have an anti-obesity effect through two different targets. Administration-dependent effects that butyrate imposes on the adipose tissue (oral administration) and microbiome (fiber-derived) make it a promising candidate for the personalized treatment of obesity.

RevDate: 2024-02-17

Liu H, Liu W, Ai M, et al (2024)

Effects of β-mannanase supplementation on productive performance, inflammation, energy metabolism, and cecum microbiota composition of laying hens fed with reduced-energy diets.

Poultry science, 103(4):103521 pii:S0032-5791(24)00100-7 [Epub ahead of print].

The objective of this study is to investigate the beneficial effects and underlying mechanism of dietary β-mannanase supplementation on the productive performance of laying hens fed with metabolic energy (ME)-reduced diets. A total of 448 Hy-Line gray laying hens were randomly assigned to seven groups. Each group had 8 replicates with 8 hens. The groups included a control diet (CON) with a ME of 2750 kcal/Kg, diets reduced by 100 kcal/Kg or 200 kcal/Kg ME (ME_100 or ME_200), and diets with 0.15 g/Kg or 0.2 g/Kg β-mannanase (ME_100+β-M_0.15, ME_100+β-M_0.2, ME_200+β-M_0.15, and ME_200+β-M_0.2). The productive performance, egg quality, intestinal morphology, inflammatory response, mRNA expression related to the Nuclear factor kappa B (NF-κB) and AMPK pathway, and cecum microbiome were evaluated in this study. ME-reduced diets negatively impacted the productive performance of laying hens. However, supplementation with β-mannanase improved FCR, decreased ADFI, and restored average egg weight to the level of the CON group. ME-reduced diets increased the levels of interleukin-1β (IL-1β) and IL-6 while decreasing the levels of IL-4 and IL-10 in the jejunum of laying hens. However, dietary β-mannanase supplementation improved jejunum morphology, reduced pro-inflammatory cytokine concentrations, and increased levels of anti-inflammatory factors in laying hens fed with ME-reduced diets. The mRNA levels of IL-6, IFN-γ, TLR4, MyD88, and NF-κB in the jejunum of ME-reduced diets were significantly higher than that in CON, dietary β-mannanase supplementation decreased these genes expression in laying hens fed with ME-reduced diets. Moreover, dietary β-mannanase supplementation also decreased the mRNA levels of AMPKα and AMPKγ, and increased the abundance of mTOR in the jejunum of laying hens fed with ME-reduced diets. Cecum microbiota analysis revealed that dietary β-mannanase increased the abundance of various beneficial bacteria (e.g., g_Pseudoflavonifractor, g_Butyricicoccus, and f_Lactobacillaceae) in laying hens fed with ME-reduced diets. In conclusion, dietary β-mannanase supplementation could improve the productive performance of laying hens fed with a ME-reduced diet by improving intestinal morphology, alleviating intestinal inflammation, changing energy metabolism-related signaling pathways, and increasing cecum-beneficial microbiota.

RevDate: 2024-02-17

Li Q, Lan Y, Yang Y, et al (2024)

Effect of luminescent materials on the biochemistry, ultrastructure, and rhizobial microbiota of Spirodela polyrhiza.

Plant physiology and biochemistry : PPB, 207:108427 pii:S0981-9428(24)00095-0 [Epub ahead of print].

Fluorescent materials and technologies have become widely used in scientific research, and due to the ability to convert light wavelengths, their application to photosynthetic organisms can affect their development by altering light quality. However, the impacts of fluorescent materials on aquatic plants and their environmental risks remain unclear. To assess the effects of luminescent materials on floating aquatic macrophytes and their rhizosphere microorganisms, 4-(di-p-tolylamino)benzaldehyde-A (DTB-A) and 4-(di-p-tolylamino)benzaldehyde-M (DTB-M) (emitting blue-green and orange-red light, respectively) were added individually and jointly to Spirodela polyrhiza cultures and set at different concentrations (1, 10, and 100 μM). Both DTB-A and DTB-M exhibited phytotoxicity, which increased with concentration under separate treatment. Moreover, the combined group exhibited obvious stress relief at 10 μM compared to the individually treated group. Fluorescence imaging showed that DTB-A and DTB-M were able to enter the cell matrix and organelles of plant leaves and roots. Peroxidation induced cellular damage, contributing to a decrease in superoxide dismutase (SOD) and peroxidase (POD) activities and malondialdehyde (MDA) accumulation. Decomposition of organelle structures, starch accumulation in chloroplasts, and plasmolysis were observed under the ultrastructure, disrupting photosynthetic pigment content and photosynthesis. DTB-A and DTB-M exposure resulted in growth inhibition, dry weight loss, and leaf yellowing in S. polyrhiza. A total of 3519 Operational Taxonomic Units (OTUs) were identified in the rhizosphere microbiome. The microbial communities were dominated by Alphaproteobacteria, Oxyphotobacteria, and Gammaproteobacteria, with the abundance and diversity varied significantly among treatment groups according to Shannon, Simpson, and Chao1 indices. This study revealed the stress defense response of S. polyrhiza to DTB-A and DTB-M exposures, which provides a broader perspective for the bioremediation of pollutants using aquatic plants and supports the further development of fluorescent materials for applications.

RevDate: 2024-02-17

Lo B, Biederman L, Rogler G, et al (2024)

Specific antibiotics increases the risk of flare-ups in patients with inflammatory bowel disease - results from a Danish nationwide population-based nested case-control study.

Journal of Crohn's & colitis pii:7609936 [Epub ahead of print].

INTRODUCTION: IBD patients have a relapsing-remitting disease course, and amongst environmental factors that aggravate the disease course, common drugs aside from NSAIDs are not studied in detail. While the microbiome is considered to play a significant role on the disease course the impact of antibiotics is poorly understood. This study investigated the potential impact of different classes of antibiotics on course of disease in IBD using the Danish National Patient Registry.

METHODS: Danish IBD patients were studied using two nested case-control cohorts exploring associations between antibiotic types and IBD flare-ups, defined as IBD-related hospitalizations and/or high-dose systemic steroid exposure. Multivariate logistic regression and eXtreme Gradient Boosted decision tree (GBDT) machine learning methods evaluated antibiotic risks.

RESULTS: Two cohorts with 15,636 and 5,178 patients were analysed for risk of hospitalisation and course of steroids, respectively.The risk of a flare-up was significantly increased with antecedent exposure to quinolones (ATC:J01M. OR:3.04-3.82), antimycotics (ATC:J02A. OR:1.50-2.30), agents against amoebiasis and protozoal infections (ATC:P01A. OR: 1.95-3.18), intestinal anti-infectives (ATC:A07A. OR:2.09-2.32) and beta-lactam antibiotics (ATC:J01C. OR:1.36).The GBDT models achieved an AUC between 0.71-0.85 for predicting flare-ups, with the same above-mentioned antibiotics being in the 10 most important variables.

CONCLUSION: We found distinctive antibiotics to be significantly associated with an increased risk of IBD flare-ups. Our findings are corroborated by our GBDT machine learning models. Healthcare providers should be aware about the deleterious potential of specific antibiotic groups in patients with IBD only using these agents in a restrictive manner or preferentially consider alternative antibiotic groups.

RevDate: 2024-02-17

Talwar C, Nagar S, RK Negi (2024)

Comparative analyses of gut microbiota reveal ammonia detoxification and nitrogen assimilation in Cyprinus carpio var. specularis.

Folia microbiologica [Epub ahead of print].

The complex niche of fish gut is often characterized by the associated microorganisms that have implications in fish gut-health nexus. Although efforts to distinguish the microbial communities have highlighted their disparate structure along the gut length, remarkably little information is available about their distinct structural and functional profiles in different gut compartments in different fish species. Here, we performed comparative taxonomic and predictive functional analyses of the foregut and hindgut microbiota in an omnivorous freshwater fish species, Cyprinus carpio var. specularis, commonly known as mirror carp. Our analyses showed that the hindgut microbiota could be distinguished from foregut based on the abundance of ammonia-oxidizing, denitrifying, and nitrogen-fixing commensals of families such as Rhodospirillaceae, Oxalobacteraceae, Nitrosomonadaceae, and Nitrospiraceae. Functionally, unique metabolic pathways such as degradation of lignin, 2-nitrobenzoate, vanillin, vanillate, and toluene predicted within hindgut also hinted at the ability of hindgut microbiota for assimilation of nitrogen and detoxification of ammonia. The study highlights a major role of hindgut microbiota in assimilating nitrogen, which remains to be one of the limiting nutrients within the gut of mirror carp.

RevDate: 2024-02-17

Yadav R, M Dharne (2024)

Utility of metagenomics for bioremediation: a comprehensive review on bioremediation mechanisms and microbial dynamics of river ecosystem.

Environmental science and pollution research international [Epub ahead of print].

Global industrialization has contributed substantial amounts of chemical pollutants in rivers, resulting in an uninhabitable state and impacting different life forms. Moreover, water macrophytes, such as water hyacinths, are abundantly present in polluted rivers, significantly affecting the overall water biogeochemistry. Bioremediation involves utilizing microbial metabolic machinery and is one of the most viable approaches for removing toxic pollutants. Conventional techniques generate limited information on the indigenous microbial population and their xenobiotic metabolism, failing the bioremediation process. Metagenomics can overcome these limitations by providing in-depth details of microbial taxa and functionality-related information required for successful biostimulation and augmentation. An in-depth summary of the findings related to pollutant metabolizing genes and enzymes in rivers still needs to be collated. The present study details bioremediation genes and enzymes functionally mined from polluted river ecosystems worldwide using a metagenomic approach. Several studies reported a wide variety of pollutant-degrading enzymes involved in the metabolism of dyes, plastics, persistent organic pollutants, and aromatic hydrocarbons. Additionally, few studies also noted a shift in the microbiome of the rivers upon exposure to contaminants, crucially affecting the ecological determinant processes. Furthermore, minimal studies have focused on the role of water-hyacinth-associated microbes in the bioremediation potentials, suggesting the need for the bioprospecting of these lesser-studied microbes. Overall, our study summarizes the prospects and utilities of the metagenomic approach and proposes the need to employ it for efficient bioremediation.

RevDate: 2024-02-17

Stuij TM, Cleary DFR, Rocha RJM, et al (2024)

Impacts of humic substances, elevated temperature and UVB radiation on bacterial communities of the marine sponge Chondrilla sp.

FEMS microbiology ecology pii:7609683 [Epub ahead of print].

Sponges are abundant components of coral reefs known for their filtration capabilities and intricate interactions with microbes. They play a crucial role in maintaining the ecological balance of coral reefs. Humic substances (HS) affect bacterial communities across terrestrial, freshwater, and marine ecosystems. However, the specific effects of HS on sponge-associated microbial symbionts have largely been neglected. Here, we used a randomized-controlled microcosm setup to investigate the independent and interactive effects of HS, elevated temperature, and UVB radiation on bacterial communities associated with the sponge Chondrilla sp. Our results indicated the presence of a core bacterial community consisting of relatively abundant members, apparently resilient to the tested environmental perturbations, alongside a variable bacterial community. Elevated temperature positively affected the relative abundances of ASVs related to Planctomycetales and members of the families Pseudohongiellaceae and Hyphomonadaceae. HS increased the relative abundances of several ASVspotentially involved in recalcitrant organic matter degradation (e.g. the BD2-11 terrestrial group, Saccharimonadales, and SAR202 clade). There was no significant independent effect of UVB and no significant interactive effects of HS, Heat and UVB on bacterial diversity and composition. The significant, independent impact of HS on the composition of sponge bacterial communities suggests that alterations to HS inputs may have cascading effects on adjacent marine ecosystems.

RevDate: 2024-02-17

Rering CC, Rudolph AB, Li QB, et al (2024)

A quantitative survey of the blueberry (Vaccinium spp.) culturable nectar microbiome: variation between cultivars, locations, and farm management approaches.

FEMS microbiology ecology pii:7609685 [Epub ahead of print].

Microbes in floral nectar can impact both their host plants and floral visitors, yet little is known about the nectar microbiome of most pollinator-dependent crops. In this study, we examined the abundance and composition of the fungi and bacteria inhabiting Vaccinium spp. nectar, as well as nectar volume and sugar concentrations. We compared wild V. myrsinites with two field-grown V. corymbosum cultivars collected from two organic and two conventional farms. Differences in nectar traits and microbiomes were identified between V. corymbosum cultivars but not Vaccinium species. The microbiome of cultivated plants also varied greatly between farms, whereas management regime had only subtle effects, with higher fungal populations detected under organic management. Nectars were hexose-dominant, and high cell densities were correlated with reduced nectar sugar concentrations. Bacteria were more common than fungi in blueberry nectar, although both were frequently detected and co-occurred more often than would be predicted by chance. 'Cosmopolitan' blueberry nectar microbes that were isolated in all plants, including Rosenbergiella sp. and Symmetrospora symmetrica, were identified. This study provides the first systematic report of the blueberry nectar microbiome, which may have important implications for pollinator and crop health.

RevDate: 2024-02-17

Bell AG, McMurtrie J, Bolaños LM, et al (2024)

Influence of host phylogeny and water physicochemistry on microbial assemblages of the fish skin microbiome.

FEMS microbiology ecology pii:7609682 [Epub ahead of print].

The skin of fish contains a diverse microbiota that has symbiotic functions with the host, facilitating pathogen exclusion, immune system priming and nutrient degradation. The composition of fish skin microbiomes varies across species and in response to a variety of stressors, however, there has been no systematic analysis across these studies to evaluate how these factors shape fish skin microbiomes. Here, we examined 1922 fish skin microbiomes from 36 studies that included 98 species and nine rearing conditions to investigate associations between fish skin microbiome, fish species, and water physiochemical factors. Proteobacteria, particularly the class Gammaproteobacteria, were present in all marine and freshwater fish skin microbiomes. Acinetobacter, Aeromonas, Ralstonia, Sphingomonas and Flavobacterium were the most abundant genera within freshwater fish skin microbiomes, and Alteromonas, Photobacterium, Pseudoalteromonas, Psychrobacter and Vibrio were the most abundant in saltwater fish. Our results show that different culturing (rearing) environments have a small but significant effect on the skin bacterial community compositions. Water temperature, pH, dissolved oxygen concentration and salinity significantly correlated with differences in beta-diversity but not necessarily alpha-diversity. To improve study comparability on fish skin microbiomes, we provide recommendations for approaches to the analyses of sequencing data and improve study reproducibility.

RevDate: 2024-02-17

Conde-Pérez K, Aja-Macaya P, Buetas E, et al (2024)

The multispecies microbial cluster of Fusobacterium, Parvimonas, Bacteroides and Faecalibacterium as a precision biomarker for colorectal cancer diagnosis.

Molecular oncology [Epub ahead of print].

The incidence of colorectal cancer (CRC) has increased worldwide, and early diagnosis is crucial to reduce mortality rates. Therefore, new noninvasive biomarkers for CRC are required. Recent studies have revealed an imbalance in the oral and gut microbiomes of patients with CRC, as well as impaired gut vascular barrier function. In the present study, the microbiomes of saliva, crevicular fluid, feces, and non-neoplastic and tumor intestinal tissue samples of 93 CRC patients and 30 healthy individuals without digestive disorders (non-CRC) were analyzed by 16S rRNA metabarcoding procedures. The data revealed that Parvimonas, Fusobacterium, and Bacteroides fragilis were significantly over-represented in stool samples of CRC patients, whereas Faecalibacterium and Blautia were significantly over-abundant in the non-CRC group. Moreover, the tumor samples were enriched in well-known periodontal anaerobes, including Fusobacterium, Parvimonas, Peptostreptococcus, Porphyromonas, and Prevotella. Co-occurrence patterns of these oral microorganisms were observed in the subgingival pocket and in the tumor tissues of CRC patients, where they also correlated with other gut microbes, such as Hungatella. This study provides new evidence that oral pathobionts, normally located in subgingival pockets, can migrate to the colon and probably aggregate with aerobic bacteria, forming synergistic consortia. Furthermore, we suggest that the group composed of Fusobacterium, Parvimonas, Bacteroides, and Faecalibacterium could be used to design an excellent noninvasive fecal test for the early diagnosis of CRC. The combination of these four genera would significantly improve the reliability of a discriminatory test with respect to others that use a single species as a unique CRC biomarker.

RevDate: 2024-02-17

Pillai P, TC Gouhier (2024)

Metamicrobiome diversity promotes the evolution of host-microbial mutualisms.

Journal of evolutionary biology pii:7609175 [Epub ahead of print].

Ecological theory suggests that a host organism's internal spatial structure can promote the persis- tence of mutualistic microbes by allowing for the turnover of tissue occupied by non-beneficial or cheating microbes. This type of regulation, whereby a host preferentially rewards tissue occupied by beneficial members of its microbiome but sanctions tissue occupied by non-beneficial cheaters, is expected to generate a competition-extinction trade-off by allowing beneficial microbes to expe- rience a lower extinction rate than competitively dominant cheaters. Using an adaptive dynamics approach, we demonstrate that although ecologically stable, microbial regulation via sanctioning is not stable in any evolutionary sense, as each individual host will be under pressure to reduce the costs incurred from cheater suppression in order to maximize its own fitness at the expense of the rest of the host population. However, increasing the diversity of non-beneficial cheaters in the host population metamicrobiome can lead to an increase in the relative fitness of hosts that actively sanction non-performing tissue, thus facilitating the evolutionary emergence and persistence of such strategies in host-microbial systems. These counterintuitive results demonstrate how diversity at multiple levels of biological organization and spatiotemporal scales can interact to facilitate the establishment and maintenance of mutualistic relationships.

RevDate: 2024-02-17

Anneberg TJ, Cullen NP, O'Neill EM, et al (2024)

Neopolyploidy has variable effects on the diversity and composition of the wild strawberry microbiome.

American journal of botany [Epub ahead of print].

PREMISE: Whole-genome duplication (neopolyploidy) can instantly differentiate the phenotype of neopolyploids from their diploid progenitors. These phenotypic shifts in organs such as roots and leaves could also differentiate the way neopolyploids interact with microbial species. While some studies have addressed how specific microbial interactions are affected by neopolyploidy, we lack an understanding of how genome duplication affects the diversity and composition of microbial communities.

METHODS: We performed a common garden experiment with multiple clones of artificially synthesized autotetraploids and their ancestral diploids, derived from 13 genotypes of wild strawberry, Fragaria vesca. We sequenced epiphytic bacteria and fungi from roots and leaves and characterized microbial communities and leaf functional traits.

RESULTS: Autotetraploidy had no effect on bacterial alpha diversity of either organ, but it did have a genotype-dependent effect on the diversity of fungi on leaves. In contrast, autotetraploidy restructured the community composition of leaf bacteria and had a genotype-dependent effect on fungal community composition in both organs. The most differentially abundant bacterial taxon on leaves belonged to the Sphingomonas, while a member of the Trichoderma was the most differentially abundant fungal taxon on roots. Ploidy-induced change in leaf size was strongly correlated with a change in bacterial but not fungal leaf communities.

CONCLUSIONS: Genome duplication can immediately alter aspects of the plant microbiome, but this effect varies by host genotype and bacterial and fungal community. Expanding these studies to wild settings where plants are exposed continuously to microbes are needed to confirm the patterns observed here.

RevDate: 2024-02-17

Huang KD, Amend L, Gálvez EJC, et al (2024)

Establishment of a non-Westernized gut microbiota in men who have sex with men is associated with sexual practices.

Cell reports. Medicine pii:S2666-3791(24)00049-1 [Epub ahead of print].

The human gut microbiota is influenced by various factors, including health status and environmental conditions, yet considerable inter-individual differences remain unexplained. Previous studies identified that the gut microbiota of men who have sex with men (MSM) is distinct from that of non-MSM. Here, we reveal through species-level microbiota analysis using shotgun metagenomics that the gut microbiota of many MSM with Western origin resembles gut microbial communities of non-Westernized populations. Specifically, MSM gut microbiomes are frequently dominated by members of the Prevotellaceae family, including co-colonization of species from the Segatella copri complex and unknown Prevotellaceae members. Questionnaire-based analysis exploring inter-individual differences in MSM links specific sexual practices to microbiota composition. Moreover, machine learning identifies microbial features associated with sexual activities in MSM. Together, this study shows associations of sexual activities with gut microbiome alterations in MSM, which may have a large impact on population-based microbiota studies.

RevDate: 2024-02-17

Liu Y, Jia N, Tang C, et al (2024)

Microglia in Microbiota-Gut-Brain Axis: A Hub in Epilepsy.

Molecular neurobiology [Epub ahead of print].

There is growing concern about the role of the microbiota-gut-brain axis in neurological illnesses, and it makes sense to consider microglia as a critical component of this axis in the context of epilepsy. Microglia, which reside in the central nervous system, are dynamic guardians that monitor brain homeostasis. Microglia receive information from the gut microbiota and function as hubs that may be involved in triggering epileptic seizures. Vagus nerve bridges the communication in the axis. Essential axis signaling molecules, such as gamma-aminobutyric acid, 5-hydroxytryptamin, and short-chain fatty acids, are currently under investigation for their participation in drug-resistant epilepsy (DRE). In this review, we explain how vagus nerve connects the gut microbiota to microglia in the brain and discuss the emerging concepts derived from this interaction. Understanding microbiota-gut-brain axis in epilepsy brings hope for DRE therapies. Future treatments can focus on the modulatory effect of the axis and target microglia in solving DRE.

RevDate: 2024-02-17

Liu HB, Sun HX, Du LQ, et al (2024)

Rice receptor kinase FLR7 regulates rhizosphere oxygen levels and enriches the dominant Anaeromyxobacter that improves submergence tolerance in rice.

The ISME journal pii:7585947 [Epub ahead of print].

Oxygen is one of the determinants of root microbiome formation. However, whether plants regulate rhizosphere oxygen levels to affect microbiota composition and the underlying molecular mechanisms remain elusive. The receptor-like kinase (RLK) family member FERONIA modulates the growth-defense tradeoff in Arabidopsis. Here, we established that rice FERONIA-like RLK 7 (FLR7) controls rhizosphere oxygen levels by methylene blue staining, oxygen flux and potential measurements. The formation of oxygen-transporting aerenchyma in roots is negatively regulated by FLR7. We further characterized the root microbiota of 11 FLR mutants including flr7 and wild-type Nipponbare (Nip) grown in the field by 16S ribosomal RNA gene profiling and demonstrated that the 11 FLRs are involved in regulating rice root microbiome formation. The most abundant anaerobic-dependent genus Anaeromyxobacter in the Nip root microbiota was less abundant in the root microbiota of all these mutants, and this contributed the most to the community differences between most mutants and Nip. Metagenomic sequencing revealed that flr7 increases aerobic respiration and decreases anaerobic respiration in the root microbiome. Finally, we showed that a representative Anaeromyxobacter strain improved submergence tolerance in rice via FLR7. Collectively, our findings indicate that FLR7 mediates changes in rhizosphere oxygen levels and enriches the beneficial dominant genus Anaeromyxobacter and may provide insights for developing plant flood prevention strategies via the use of environment-specific functional soil microorganisms.

RevDate: 2024-02-19

Hu J, Chen J, Ma L, et al (2024)

Characterizing core microbiota and regulatory functions of the pig gut microbiome.

The ISME journal, 18(1): [Epub ahead of print].

Domestic pigs (Sus scrofa) are the leading terrestrial animals used for meat production. The gut microbiota significantly affect host nutrition, metabolism, and immunity. Hence, characterization of the gut microbial structure and function will improve our understanding of gut microbial resources and the mechanisms underlying host-microbe interactions. Here, we investigated the gut microbiomes of seven pig breeds using metagenomics and 16S rRNA gene amplicon sequencing. We established an expanded gut microbial reference catalog comprising 17 020 160 genes and identified 4910 metagenome-assembled genomes (MAGs). We also analyzed the gut resistome to provide an overview of the profiles of the antimicrobial resistance genes in pigs. By analyzing the relative abundances of microbes, we identified three core-predominant gut microbes (Phascolarctobacterium succinatutens, Prevotella copri, and Oscillibacter valericigenes) in pigs used in this study. Oral administration of the three core-predominant gut microbes significantly increased the organ indexes (including the heart, spleen, and thymus), but decreased the gastrointestinal lengths in germ-free (GF) mice. The three core microbes significantly enhanced intestinal epithelial barrier function and altered the intestinal mucosal morphology, as was evident from the increase in crypt depths in the duodenum and ileum. Furthermore, the three core microbes significantly affected several metabolic pathways (such as "steroid hormone biosynthesis", "primary bile acid biosynthesis", "phenylalanine, tyrosine and tryptophan biosynthesis", and "phenylalanine metabolism") in GF mice. These findings provide a panoramic view of the pig gut microbiome and insights into the functional contributions of the core-predominant gut microbes to the host.

RevDate: 2024-02-17

Dion MB, Shah SA, Deng L, et al (2024)

Escherichia coli CRISPR arrays from early life fecal samples preferentially target prophages.

The ISME journal pii:7536056 [Epub ahead of print].

CRISPR-Cas systems are defense mechanisms against phages and other nucleic acids that invade bacteria and archaea. In Escherichia coli, it is generally accepted that CRISPR-Cas systems are inactive in laboratory conditions due to a transcriptional repressor. In natural isolates, it has been shown that CRISPR arrays remain stable over the years and that most spacer targets (protospacers) remain unknown. Here, we re-examine CRISPR arrays in natural E. coli isolates and investigate viral and bacterial genomes for spacer targets using a bioinformatics approach coupled to a unique biological dataset. We first sequenced the CRISPR1 array of 1769 E. coli isolates from the fecal samples of 639 children obtained during their first year of life. We built a network with edges between isolates that reflect the number of shared spacers. The isolates grouped into 34 modules. A search for matching spacers in bacterial genomes showed that E. coli spacers almost exclusively target prophages. While we found instances of self-targeting spacers, those involving a prophage and a spacer within the same bacterial genome were rare. The extensive search for matching spacers also expanded the library of known E. coli protospacers to 60%. Altogether, these results suggest that E. coli's CRISPR-Cas is an anti-prophage system and highlight the importance of reconsidering the criteria use to deem CRISPR-Cas systems active.

RevDate: 2024-02-17

Popovic A, Cao EY, Han J, et al (2024)

Commensal protist Tritrichomonas musculus exhibits a dynamic life cycle that induces extensive remodeling of the gut microbiota.

The ISME journal pii:7601004 [Epub ahead of print].

Commensal protists and gut bacterial communities exhibit complex relationships, mediated at least in part through host immunity. To improve our understanding of this tripartite interplay, we investigated community and functional dynamics between the murine protist Tritrichomonas musculus (Tmu) and intestinal bacteria in healthy and B cell-deficient mice. We identified dramatic, protist-driven remodeling of resident microbiome growth and activities, in parallel with Tmu functional changes, which were accelerated in the absence of B cells. Metatranscriptomic data revealed nutrient-based competition between bacteria and the protist. Single cell transcriptomics identified distinct Tmu life stages, providing new evidence for trichomonad sexual replication and the formation of pseudocysts. Unique cell states were validated in situ through microscopy and flow cytometry. Our results reveal complex microbial dynamics during the establishment of a commensal protist in the gut, and provide valuable datasets to drive future mechanistic studies.

RevDate: 2024-02-17

Nelson C, Dadi P, Shah DD, et al (2024)

Spatial organization of a soil cyanobacterium and its cyanosphere through GABA/Glu signaling to optimize mutualistic nitrogen fixation.

The ISME journal pii:7560352 [Epub ahead of print].

Soil biocrusts are characterized by the spatial self-organization of resident microbial populations at small scales. The cyanobacterium Microcoleus vaginatus, a prominent primary producer and pioneer biocrust former, relies on a mutualistic carbon (C) for nitrogen (N) exchange with its heterotrophic cyanosphere microbiome, a mutualism that may be optimized through the ability of the cyanobacterium to aggregate into bundles of trichomes. Testing both environmental populations and representative isolates, we show that the proximity of mutualistic diazotroph populations results in M. vaginatus bundle formation orchestrated through chemophobic and chemokinetic responses to Gamma-aminobutyric acid (GABA) /Glutamate (Glu) signals. The signaling system is characterized by: 1) high GABA sensitivity (nM range) and low Glu sensitivity (μM - mM); 2) GABA and Glu are produced by the cyanobacterium as an autoinduction response to N deficiency; and 3) interspecific signaling by heterotrophs in response to C limitation. Further, it crucially switches from a positive to a negative feed-back loop with increasing GABA concentration, thus setting maximal bundle sizes. The unprecedented use of GABA/Glu as an intra- and interspecific signal in the spatial organization of microbiomes highlights the pair as truly universal infochemicals.

RevDate: 2024-02-20
CmpDate: 2024-02-19

Fernández-Pato A, Sinha T, Gacesa R, et al (2024)

Choice of DNA extraction method affects stool microbiome recovery and subsequent phenotypic association analyses.

Scientific reports, 14(1):3911.

The lack of standardization in the methods of DNA extraction from fecal samples represents the major source of experimental variation in the microbiome research field. In this study, we aimed to compare the metagenomic profiles and microbiome-phenotype associations obtained by applying two commercially available DNA extraction kits: the AllPrep DNA/RNA Mini Kit (APK) and the QIAamp Fast DNA Stool Mini Kit (FSK). Using metagenomic sequencing data available from 745 paired fecal samples from two independent population cohorts, Lifelines-DEEP (LLD, n = 292) and the 500 Functional Genomics project (500FG, n = 453), we confirmed significant differences in DNA yield and the recovered microbial communities between protocols, with the APK method resulting in a higher DNA concentration and microbial diversity. Further, we observed a massive difference in bacterial relative abundances at species-level between the APK and the FSK protocols, with > 75% of species differentially abundant between protocols in both cohorts. Specifically, comparison with a standard mock community revealed that the APK method provided higher accuracy in the recovery of microbial relative abundances, with the absence of a bead-beating step in the FSK protocol causing an underrepresentation of gram-positive bacteria. This heterogeneity in the recovered microbial composition led to remarkable differences in the association with anthropometric and lifestyle phenotypes. The results of this study further reinforce that the choice of DNA extraction method impacts the metagenomic profile of human gut microbiota and highlight the importance of harmonizing protocols in microbiome studies.

RevDate: 2024-02-17

Du X, Liu N, Yan B, et al (2024)

Proximity-based defensive mutualism between Streptomyces and Mesorhizobium by sharing and sequestering iron.

The ISME journal pii:7513082 [Epub ahead of print].

Microorganisms living in soil maintain intricate interactions among themselves, forming the soil microbiota that influences the rhizosphere microbiome and plant growth. However, the mechanisms underlying the soil microbial interactions remain unclear. Streptomyces and Mesorhizobium are commonly found in soil and serve as plant growth-promoting rhizobacteria (PGPR). Here, we identified an unprecedented interaction between the colonies of red-soil-derived Streptomyces sp. FXJ1.4098 and Mesorhizobium sp. BAC0120 and referred to it as "proximity-based defensive mutualism (PBDM)". We found that metabolite-mediated iron competition and sharing between the two microorganisms was responsible for PBDM. S. sp. FXJ1.4098 produced a highly diffusible siderophore, desferrioxamine (DFO), which made iron unavailable to co-cultured M. sp. BAC0120, thereby inhibiting its growth. S. sp. FXJ1.4098 also released poorly diffusible iron-porphyrin complexes, which could be utilized by M. sp. BAC0120, thereby restoring the growth of nearby M. sp. BAC0120. Furthermore, in ternary interactions, the PBDM strategy contributed to the protection of M. sp. BAC0120 close to S. sp. FXJ1.4098 from other microbial competitors, resulting in the coexistence of these two PGPR. A scale-up pairwise interaction screening suggested that the PBDM strategy may be common between Mesorhizobium and red-soil-derived Streptomyces. These results demonstrate the key role of iron in complex microbial interactions and provide novel insights into the coexistence of PGPR in soil.

RevDate: 2024-02-16

Dong PT, Tian J, Kobayashi-Kirschvink KJ, et al (2024)

Episymbiotic Saccharibacteria induce intracellular lipid droplet production in their host bacteria.

The ISME journal pii:7513100 [Epub ahead of print].

Saccharibacteria (formerly TM7) are a group of widespread and genetically diverse ultrasmall bacteria with highly reduced genomes that belong to Candidate Phyla Radiation, a large monophyletic lineage with poorly understood biology. Nanosynbacter lyticus type strain TM7x is the first Saccharibacteria member isolated from the human oral microbiome. With restrained metabolic capacities, TM7x lives on the surface of, and forms an obligate episymbiotic relationship with its bacterial host, Schaalia odontolytica strain XH001. The symbiosis allows TM7x to propagate but presents a burden to host bacteria by inducing stress response. Here, we employed super-resolution fluorescence imaging to investigate the physical association between TM7x and XH001. We showed that the binding with TM7x led to a substantial alteration in the membrane fluidity of XH001. We also revealed the formation of intracellular lipid droplets (LDs) in XH001 when forming episymbiosis with TM7x, a feature that has not been reported in oral bacteria. The TM7x-induced LDs accumulation in XH001 was confirmed by label-free Raman spectroscopy, which also unveiled additional phenotypical features when XH001 cells are physically associated with TM7x. Further exploration through culturing XH001 under various stress conditions showed that LDs accumulation was a general response to stress. A survival assay demonstrated that the presence of LDs plays a protective role in XH001, enhancing its survival under adverse conditions. In conclusion, our study sheds new light on the intricate interaction between Saccharibacteria and their host bacterium, highlighting the potential benefit conferred by TM7x to its host, and further emphasizing the context-dependent nature of symbiotic relationships.

RevDate: 2024-02-20
CmpDate: 2024-02-19

Paes da Costa D, das Graças Espíndola da Silva T, Sérgio Ferreira Araujo A, et al (2024)

Soil fertility impact on recruitment and diversity of the soil microbiome in sub-humid tropical pastures in Northeastern Brazil.

Scientific reports, 14(1):3919.

Soil fertility is key point to pastures systems and drives the microbial communities and their functionality. Therefore, an understanding of the interaction between soil fertility and microbial communities can increase our ability to manage pasturelands and maintain their soil functioning and productivity. This study probed the influence of soil fertility on microbial communities in tropical pastures in Brazil. Soil samples, gathered from the top 20 cm of twelve distinct areas with diverse fertility levels, were analyzed via 16S rRNA sequencing. The soils were subsequently classified into two categories, namely high fertility (HF) and low fertility (LF), using the K-Means clustering. The random forest analysis revealed that high fertility (HF) soils had more bacterial diversity, predominantly Proteobacteria, Nitrospira, Chloroflexi, and Bacteroidetes, while Acidobacteria increased in low fertility (LF) soils. High fertility (HF) soils exhibited more complex network interactions and an enrichment of nitrogen-cycling bacterial groups. Additionally, functional annotation based on 16S rRNA varied between clusters. Microbial groups in HF soil demonstrated enhanced functions such as nitrate reduction, aerobic ammonia oxidation, and aromatic compound degradation. In contrast, in the LF soil, the predominant processes were ureolysis, cellulolysis, methanol oxidation, and methanotrophy. Our findings expand our knowledge about how soil fertility drives bacterial communities in pastures.

RevDate: 2024-02-16

Björk JR, Bolte LA, Maltez Thomas A, et al (2024)

Longitudinal gut microbiome changes in immune checkpoint blockade-treated advanced melanoma.

Nature medicine [Epub ahead of print].

Multiple clinical trials targeting the gut microbiome are being conducted to optimize treatment outcomes for immune checkpoint blockade (ICB). To improve the success of these interventions, understanding gut microbiome changes during ICB is urgently needed. Here through longitudinal microbiome profiling of 175 patients treated with ICB for advanced melanoma, we show that several microbial species-level genome bins (SGBs) and pathways exhibit distinct patterns from baseline in patients achieving progression-free survival (PFS) of 12 months or longer (PFS ≥12) versus patients with PFS shorter than 12 months (PFS <12). Out of 99 SGBs that could discriminate between these two groups, 20 were differentially abundant only at baseline, while 42 were differentially abundant only after treatment initiation. We identify five and four SGBs that had consistently higher abundances in patients with PFS ≥12 and <12 months, respectively. Constructing a log ratio of these SGBs, we find an association with overall survival. Finally, we find different microbial dynamics in different clinical contexts including the type of ICB regimen, development of immune-related adverse events and concomitant medication use. Insights into the longitudinal dynamics of the gut microbiome in association with host factors and treatment regimens will be critical for guiding rational microbiome-targeted therapies aimed at enhancing ICB efficacy.

RevDate: 2024-02-20
CmpDate: 2024-02-19

Peña-Cearra A, Palacios A, Pellon A, et al (2024)

Akkermansia muciniphila-induced trained immune phenotype increases bacterial intracellular survival and attenuates inflammation.

Communications biology, 7(1):192.

The initial exposure to pathogens and commensals confers innate immune cells the capacity to respond distinctively upon a second stimulus. This training capacity might play key functions in developing an adequate innate immune response to the continuous exposure to bacteria. However, the mechanisms involved in induction of trained immunity by commensals remain mostly unexplored. A. muciniphila represents an attractive candidate to study the promotion of these long-term responses. Here, we show that priming of macrophages with live A. muciniphila enhances bacterial intracellular survival and decreases the release of pro- and anti-inflammatory signals, lowering the production of TNF and IL-10. Global transcriptional analysis of macrophages after a secondary exposure to the bacteria showed the transcriptional rearrangement underpinning the phenotype observed compared to acutely exposed cells, with the increased expression of genes related to phagocytic capacity and those involved in the metabolic adjustment conducing to innate immune training. Accordingly, key genes related to bacterial killing and pro-inflammatory pathways were downregulated. These data demonstrate the importance of specific bacterial members in the modulation of local long-term innate immune responses, broadening our knowledge of the association between gut microbiome commensals and trained immunity as well as the anti-inflammatory probiotic potential of A. muciniphila.


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In the early 1990's, Robert Robbins was a faculty member at Johns Hopkins, where he directed the informatics core of GDB — the human gene-mapping database of the international human genome project. To share papers with colleagues around the world, he set up a small paper-sharing section on his personal web page. This small project evolved into The Electronic Scholarly Publishing Project.

ESP Support

In 1995, Robbins became the VP/IT of the Fred Hutchinson Cancer Research Center in Seattle, WA. Soon after arriving in Seattle, Robbins secured funding, through the ELSI component of the US Human Genome Project, to create the original ESP.ORG web site, with the formal goal of providing free, world-wide access to the literature of classical genetics.

ESP Rationale

Although the methods of molecular biology can seem almost magical to the uninitiated, the original techniques of classical genetics are readily appreciated by one and all: cross individuals that differ in some inherited trait, collect all of the progeny, score their attributes, and propose mechanisms to explain the patterns of inheritance observed.

ESP Goal

In reading the early works of classical genetics, one is drawn, almost inexorably, into ever more complex models, until molecular explanations begin to seem both necessary and natural. At that point, the tools for understanding genome research are at hand. Assisting readers reach this point was the original goal of The Electronic Scholarly Publishing Project.

ESP Usage

Usage of the site grew rapidly and has remained high. Faculty began to use the site for their assigned readings. Other on-line publishers, ranging from The New York Times to Nature referenced ESP materials in their own publications. Nobel laureates (e.g., Joshua Lederberg) regularly used the site and even wrote to suggest changes and improvements.

ESP Content

When the site began, no journals were making their early content available in digital format. As a result, ESP was obliged to digitize classic literature before it could be made available. For many important papers — such as Mendel's original paper or the first genetic map — ESP had to produce entirely new typeset versions of the works, if they were to be available in a high-quality format.

ESP Help

Early support from the DOE component of the Human Genome Project was critically important for getting the ESP project on a firm foundation. Since that funding ended (nearly 20 years ago), the project has been operated as a purely volunteer effort. Anyone wishing to assist in these efforts should send an email to Robbins.

ESP Plans

With the development of methods for adding typeset side notes to PDF files, the ESP project now plans to add annotated versions of some classical papers to its holdings. We also plan to add new reference and pedagogical material. We have already started providing regularly updated, comprehensive bibliographies to the ESP.ORG site.

Electronic Scholarly Publishing
961 Red Tail Lane
Bellingham, WA 98226

E-mail: RJR8222 @

Papers in Classical Genetics

The ESP began as an effort to share a handful of key papers from the early days of classical genetics. Now the collection has grown to include hundreds of papers, in full-text format.

Digital Books

Along with papers on classical genetics, ESP offers a collection of full-text digital books, including many works by Darwin and even a collection of poetry — Chicago Poems by Carl Sandburg.


ESP now offers a large collection of user-selected side-by-side timelines (e.g., all science vs. all other categories, or arts and culture vs. world history), designed to provide a comparative context for appreciating world events.


Biographical information about many key scientists (e.g., Walter Sutton).

Selected Bibliographies

Bibliographies on several topics of potential interest to the ESP community are automatically maintained and generated on the ESP site.

ESP Picks from Around the Web (updated 07 JUL 2018 )