Taxonomic Differences Research Articles

Pasture management intensification shifts the soil microbiome composition and ecosystem functions

Natural grasslands are important reservoirs of animal and plant biodiversity and provide several ecosystem services, through the action of soil microorganisms. The increased demand for food, energy, and cattle activity has led to the conversion of natural grasslands to cultivated systems. However, the consequences of this conversion for soil microbial diversity and ecosystem functioning are yet to be discovered. Here, we used the 16 S rRNA amplicon sequencing and a large set of soil and environmental variables to understand the possible effects of natural grasslands to cultivated pasture conversion on the soil microbial structure, composition, diversity, and functions. The study areas followed a gradient of increasing soil disturbance intensity, as follows: Natural grassland (NG), Improved-natural grassland (IG), Perennial-cultivated pasture (PP), and Annual-cultivated pasture (AP). Natural grassland conversion to managed and cultivated pastures decreased the abundances of Acidobacteria and Verrucomicrobia, while increased α-, γ-, and δ-Proteobacteria, Gemmatimonadetes, Bacteroidetes, Patescibacteria, and Latescibacteria. The predicted functional profiles have also changed, as functions like ‘cellulolytic and symbionts/parasites’ decreased after natural to cultivated pastures conversion, while ‘nitrogen respiration’, ‘sulfur respiration’, and ‘aromatic compound degradation’ functions increased. Aboveground plant diversity decrease influenced belowground microbial diversity. The main drivers of diversity, composition, and functional potential are associated with soil attributes affected by liming, like aluminum complexation. In conclusion, we have found taxonomic and functional differences between natural and managed grasslands (NG and IG, respectively) and cultivated pastures (PP and AP), with consequences for management strategies and biodiversity conservation priorities.

Inferring Bacterial Community Interactions and Functionalities Associated with Osteopenia and Osteoporosis in Taiwanese Postmenopausal Women.

Growing evidence suggests that the gut microbiota and their metabolites are associated with bone homeostasis and fragility. However, this association is limited to microbial taxonomic differences. This study aimed to explore whether gut bacterial community associations, composition, and functions are associated with osteopenia and osteoporosis. We compared the gut bacterial community composition and interactions of healthy postmenopausal women with normal bone density (n = 8) with those of postmenopausal women with osteopenia (n = 18) and osteoporosis (n = 21) through 16S rRNA sequencing coupled with network biology and statistical analyses. The results of this study showed reduced alpha diversity in patients with osteoporosis, followed by that in patients with osteopenia, then in healthy controls. Taxonomic analysis revealed that significantly enriched bacterial genera with higher abundance was observed in patients with osteoporosis and osteopenia than in healthy subjects. Additionally, a co-occurrence network revealed that, compared to healthy controls, bacterial interactions were higher in patients with osteoporosis, followed by those with osteopenia. Further, NetShift analysis showed that a higher number of bacteria drove changes in the microbial community structure of patients with osteoporosis than osteopenia. Correlation analysis revealed that most of these driver bacteria had a significant positive relationship with several significant metabolic pathways. Further, ordination analysis revealed that height and T-score were the primary variables influencing the gut microbial community structure. Taken together, this study evaluated that microbial community interaction is more important than the taxonomic differences in knowing the critical role of gut microbiota in postmenopausal women associated with osteopenia and osteoporosis. Additionally, the significantly enriched bacteria and functional pathways might be potential biomarkers for the prognosis and treatment of postmenopausal women with osteopenia and osteoporosis.

The bovine foot skin microbiota is associated with host genotype and the development of infectious digital dermatitis lesions

BackgroundBovine Digital Dermatitis (BDD) is a prevalent infectious disease, causing painful foot skin lesions and lameness in cattle. We describe herein the bovine foot skin microbiota and its associations with BDD using 16S rRNA gene amplicon and shotgun metagenomic sequencing on samples from 259 dairy cows from three UK dairy farms.ResultsWe show evidence of dysbiosis, and differences in taxonomy and functional profiles in the bovine foot skin microbiome of clinically healthy animals that subsequently develop BDD lesions, compared to those that do not. Our results suggest that taxonomical and functional differences together with alterations in ecological interactions between bacteria in the normal foot skin microbiome may predispose an animal to develop BDD lesions. Using genome-wide association and regional heritability mapping approaches, we provide first evidence for interactions between host genotype and certain members of the foot skin microbiota. We show the existence of significant genetic variation in the relative abundance of Treponema spp. and Peptoclostridium spp. and identify regions in the bovine genome that explain a significant proportion of this variation.ConclusionsCollectively this work shows early changes in taxonomic and functional profiles of the bovine foot-skin microbiota in clinically healthy animals which are associated with subsequent development of BDD and could be relevant to prevention of disease. The description of host genetic control of members of the foot skin microbiota, combined with the association of the latter with BDD development offer new insights into a complex relationship that can be exploited in selective breeding programmes.ApfTUdsqPmkzyTqVTTd38-Video

The influence of a probiotic/prebiotic supplement on microbial and metabolic parameters of equine cecal fluid or fecal slurry in vitro.

The microbes that reside within the equine hindgut create a complex and dynamic ecosystem. The equine hindgut microbiota is intimately associated with health and, as such, represents an area which can be beneficially modified. Synbiotics, supplements that combine probiotic micro-organisms with prebiotic ingredients, are a potential means of influencing the hindgut microbiota to promote health and prevent disease. The objective of the current study was to evaluate the influence of an equine probiotic/prebiotic supplement on characteristics of the microbiota and metabolite production in vitro. Equine cecal fluid and fecal material were collected from an abattoir in QC, CAN. Five hundred milliliters of cecal fluid was used to inoculate chemostat vessels maintained as batch fermenters (chemostat cecal, N = 11) with either 0 g (control) or 0.44 g of supplement added at 12 h intervals. One hundred milliliters of cecal fluid (anaerobic cecal, N = 15) or 5% fecal slurry (anaerobic fecal, N = 6) were maintained in an anaerobic chamber with either 0 g (control) or 0.356 g of supplement added at the time of vessel establishment. Samples were taken from vessels at vessel establishment (0), 24, or 48 h of incubation. Illumina sequencing of the V4 region of the 16S rRNA gene and bioinformatics were performed for microbiome analysis. Metabolite data was obtained via NMR spectroscopy. All statistical analyses were run in SAS 9.4. There was no effect of treatment at 24 or 48h on alpha or beta diversity indices and limited taxonomic differences were noted. Acetate, propionate, and butyrate were higher in treated compared to untreated vessels in all methods. A consistent effect of supplementation on the metabolic profile with no discernable impact on the microbiota of these in vitro systems indicates inoculum microbe viability and a utilization of the provided fermentable substrate within the systems. Although no changes within the microbiome were apparent, the consistent changes in metabolites indicates a potential prebiotic effect of the added supplement and merits further exploration.

Water quality and antibiotic resistance in the recreational waters

The overuse and improper disposal of antibiotics results in antibiotic resistance. This raises concern over the presence of antibiotic resistant bacteria (ARB) in waterways and pose health risks of antibiotic resistant infections to water recreationists. The purpose of this study was to monitor water quality, microbial ecology, and antibiotic resistance in water and biofilm on submerged plastics at two public boat launches in southeastern Louisiana. Water and biofilm samples were collected once a month, in triplicate, from two public boat launches in Louisiana, USA for a year. Water quality metrics included nitrate, ammonia, sulfate, phosphate, and organic carbon. Water samples were tested for total and fecal coliform abundance and the presence of ARB. Out of 131 bacterial isolates studied from these two sites, 86% of them tested positive for antibiotic resistance with multi-drug resistance. Antibiotic resistance genes (ARGs) for sulfonamide (sul2), bacitracin (bacA) and ampicillin (ampA) were identified in bacterial isolates from water and biofilm samples at both sites. Molecular genetic diversity analysis identified distinct taxonomic diversity differences in biofilm bacteria compared to the planktonic bacteria in the surrounding water. Biofilm samples showed increased diversity at the phylum, genus, and species levels.

TAMPA: interpretable analysis and visualization of metagenomics-based taxon abundance profiles.

Metagenomic taxonomic profiling aims to predict the identity and relative abundance of taxa in a given whole-genome sequencing metagenomic sample. A recent surge in computational methods that aim to accurately estimate taxonomic profiles, called taxonomic profilers, has motivated community-driven efforts to create standardized benchmarking datasets and platforms, standardized taxonomic profile formats, and a benchmarking platform to assess tool performance. While this standardization is essential, there is currently a lack of tools to visualize the standardized output of the many existing taxonomic profilers. Thus, benchmarking studies rely on a single-value metrics to compare performance of tools and compare to benchmarking datasets. This is one of the major problems in analyzing metagenomic profiling data, since single metrics, such as the F1 score, fail to capture the biological differences between the datasets. Here we report the development of TAMPA (Taxonomic metagenome profiling evaluation), a robust and easy-to-use method that allows scientists to easily interpret and interact with taxonomic profiles produced by the many different taxonomic profiler methods beyond the standard metrics used by the scientific community. We demonstrate the unique ability of TAMPA to generate a novel biological hypothesis by highlighting the taxonomic differences between samples otherwise missed by commonly utilized metrics. In this study, we show that TAMPA can help visualize the output of taxonomic profilers, enabling biologists to effectively choose the most appropriate profiling method to use on their metagenomics data. TAMPA is available on GitHub, Bioconda, and Galaxy Toolshed at https://github.com/dkoslicki/TAMPA and is released under the MIT license.

Construction of a compound microbial agent for biocontrol against Fusarium wilt of banana.

Banana wilt caused by Fusarium oxysporum f. sp. cubense has devastated a large number of banana plantations worldwide. Biological control is a possible method to conquer this disease. However, the control effect was often low and unstable while a single biocontrol strain had been applied in the field. Therefore, this study aimed to construct an effective compound microbial agent to control Fusarium wilt of banana (FWB) in the field. In addition to it, the compounding strategy of combining single strains for improving the control effect was investigated. Based on the compatibility test, five representative biocontrol strains were selected for the combination of all possible permutations. The pot experiment indicated that every biocontrol strain and their 26 combinations could control FWB to varying degrees. The control effect of combinations on FWB was higher than that of a single strain. In terms of the number of combinatorial biocontrol strains, the control effect of the four-strain combinations was the highest. According to the taxonomic differences of the five biocontrol strains, 26 biocontrol strain combinations could be divided into four groups. Among the strains in the combination, the larger the taxonomic differences the more easily it was to obtain a higher control effect. To obtain stable and efficient combinations, eight combinations were selected out and evaluated for their effectiveness in controlling FWB in different type soil. Compared with the other seven combinations, the four-strain combination T28 (Pt05 + Bc11 + Ba62 + gz-2) got the highest and stablest control effect in the four types of soil in greenhouse. And then the control effect of combination T28 was evaluated in field conditions, compared with commercially agents Bacillus subtilis, Trichoderma harzianum, and carbendazim. After four consecutive applications in the field, the control effect of T28 against FWB was the highest, reaching 57.14%. The results showed that combination T28 had a good application prospect, and the finding provided a reference for the construction of compound microbial agents.

Screening of potential microbial markers for lung cancer using metagenomic sequencing.

Lung cancer is the most prevalent cancer with high mortality in China, and it is associated with the dysbiosis of the lung microbiome. This study attempted to screen for specific microorganisms as potential biomarkers for distinguishing benign lung disease from lung cancer. Bronchoalveolar lavage fluid (BALF) sample was selected in the study instead of saliva to avoid contamination with oral microorganisms, and microbial taxonomic and functional differences in BALF samples from patients with lung cancer and those with those from patients with benign lung diseases were performed based on metagenomic next-generation sequencing, for the first time, so that microorganisms other than bacteria could be included. The results showed that the intrasample diversity of malignant samples was different from benign samples, and the microbial differences among malignant samples were smaller, with lower microbial diversity, significantly changed microbial abundance and metabolic functions. Metabolic function analysis revealed amino acid-related metabolism was more prevalent in benign samples, whereas carbohydrate-related metabolism was more prevalent in malignant samples. By LEfSe, Metastat and Random Forest analysis, we identified a series of important differential microorganisms. Importantly, the model combining five key genera plus one tumor marker (neuron-specific enolase) as indicators presented the optimal disease typing performance. Thus results suggest the value of these differential microorganisms enriched in tumors in mechanism research and may be potential new targets for lung cancer therapy. More importantly, the biomarkers identified in this study can be conducive to improve the clinical diagnosis of lung cancer and have good application prospects.

Analysis of bronchoalveolar lavage fluid metatranscriptomes among patients with COVID-19 disease

To better understand the potential relationship between COVID-19 disease and hologenome microbial community dynamics and functional profiles, we conducted a multivariate taxonomic and functional microbiome comparison of publicly available human bronchoalveolar lavage fluid (BALF) metatranscriptome samples amongst COVID-19 (n = 32), community acquired pneumonia (CAP) (n = 25), and uninfected samples (n = 29). We then performed a stratified analysis based on mortality amongst the COVID-19 cohort with known outcomes of deceased (n = 10) versus survived (n = 15). Our overarching hypothesis was that there are detectable and functionally significant relationships between BALF microbial metatranscriptomes and the severity of COVID-19 disease onset and progression. We observed 34 functionally discriminant gene ontology (GO) terms in COVID-19 disease compared to the CAP and uninfected cohorts, and 21 GO terms functionally discriminant to COVID-19 mortality (q < 0.05). GO terms enriched in the COVID-19 disease cohort included hydrolase activity, and significant GO terms under the parental terms of biological regulation, viral process, and interspecies interaction between organisms. Notable GO terms associated with COVID-19 mortality included nucleobase-containing compound biosynthetic process, organonitrogen compound catabolic process, pyrimidine-containing compound biosynthetic process, and DNA recombination, RNA binding, magnesium and zinc ion binding, oxidoreductase activity, and endopeptidase activity. A Dirichlet multinomial mixtures clustering analysis resulted in a best model fit using three distinct clusters that were significantly associated with COVID-19 disease and mortality. We additionally observed discriminant taxonomic differences associated with COVID-19 disease and mortality in the genus Sphingomonas, belonging to the Sphingomonadacae family, Variovorax, belonging to the Comamonadaceae family, and in the class Bacteroidia, belonging to the order Bacteroidales. To our knowledge, this is the first study to evaluate significant differences in taxonomic and functional signatures between BALF metatranscriptomes from COVID-19, CAP, and uninfected cohorts, as well as associating these taxa and microbial gene functions with COVID-19 mortality. Collectively, while this data does not speak to causality nor directionality of the association, it does demonstrate a significant relationship between the human microbiome and COVID-19. The results from this study have rendered testable hypotheses that warrant further investigation to better understand the causality and directionality of host–microbiome–pathogen interactions.

Abstract IA020: The gut microbiome in colorectal cancer

Abstract The gut microbiome plays important roles in colorectal cancer (CRC) initiation, treatment, and survivorship. This talk will highlight preliminary results from two pilot studies: Gut microbiome &amp; Oral fluoropyrimidines (GO) and Lifestyle and Outcome in Gastrointestinal Cancer (LOGIC). GO investigated the impact of oral fluoropyrimidines (e.g., capecitabine) on gut microbes via longitudinal stool sampling. Despite marked inter- and intra-individual differences in diversity and community structure, we detected multiple consistent taxonomic differences. LOGIC asked: how do diet and lifestyle, measured by the American Cancer Society (ACS) score, correlate with gut microbiota characteristics in CRC survivors? We found that components of the ACS score related to fruit and vegetable consumption, but not the overall ACS score, significantly associated with variations in microbial community structures, diversity, and differences in abundance of microorganisms at various taxonomic levels. Practical considerations influencing the design of follow-up studies in progress will be discussed. Citation Format: Chloe E. Atreya. The gut microbiome in colorectal cancer [abstract]. In: Proceedings of the AACR Special Conference on Colorectal Cancer; 2022 Oct 1-4; Portland, OR. Philadelphia (PA): AACR; Cancer Res 2022;82(23 Suppl_1):Abstract nr IA020.

Characterization of pig skin microbiome and appraisal as an in vivo subcutaneous injection model.

Pig skin is commonly used in the medical industry as an injection model due to its compelling physiological affinity to human skin. However, the pig neck skin microflora remains largely uncharacterized, which may have undesirable implications for the translatability of results to humans. This study aimed to characterize pig neck skin microbiome with direct comparison with human skin microflora at emblematic injection sites to appraise its suitability as an injection model. Ten minipigs were sampled with tape strips and swabs and analysed by matrix-assisted laser desorption/ionization-time of flight mass spectrometry and 16S/ITS high throughput sequencing and confocal laser scanning microscopy. Results were directly compared with previous investigations of human injection sites. Pig skin was dominated by phyla 94.8% Firmicutes, 3% Proteobacteria, and 2.2% Actinobacteria. Staphylococcus spp. prevailed (44.4%) at the genus level with S. capitis and S. chromogenes present in all samples. Pig skin revealed populations in the 104 colony-forming units (CFU)/cm2 range with 3% identified as Gram-negative and increased alpha diversity (compared with 102 CFU/cm2 and 10% in humans). While notable taxonomical differences on species levels were seen, pig skin encompassed 97.1% of genera found in human samples. The increased population and variation found support the pig neck as an imperfect but fidelitous subcutaneous injection model that can adequately challenge devices from a microbial standpoint.

Abstract 13266: Sex Specific Differences in the Gut Microbiome in Patients With Pulmonary Arterial Hypertension

Introduction: Pulmonary arterial hypertension (PAH) patients exhibit sexual dimorphism in pulmonary vascular remodeling and right ventricular (RV) dysfunction. While female PAH patients have severe pulmonary vascular remodeling, male PAH patients have worse RV function. Inflammation, a key component of PAH pathobiology, has been implicated as a potential mechanism for sexual dimorphism. Gut dysbiosis causes systemic inflammation. However, it is unknown whether gut dysbiosis contributes to sexual dimorphism in PAH. Hypothesis: There are sex-specific differences in the gut microbiome and microbial metabolites of PAH patients. Methods: 16S ribosomal ribonucleic acid gene sequencing was performed on stool samples from PAH patients (n=73). Markers of inflammation and circulating microbial metabolites were measured using plasma samples. Results: There was no significant difference in the Shannon diversity indices or species richness (Chao1 indices) between the gut microbiomes of male and female PAH patients. Moreover, principal component analysis of pairwise Bray-Curtis dissimilarity indices revealed no distinct microbiome compositions dependent on sex. There was no difference in serum claudin-3, a marker of gut permeability, and serum interleukin 6 levels between male and female PAH patients. When examining microbial metabolites, including trimethylamine N-oxide, short chain fatty acids, and secondary bile acids, no sex-specific differences were observed. Linear discriminant analysis of effect size revealed that there were no taxonomic differences based on sex. Conclusions: Male and female PAH patients do not possess distinct differences in their gut microbiomes or metabolites. There are also no sex-specific taxonomic differences. These findings do not support our hypothesis that gut dysbiosis may serve as a possible explanation for the sexual dimorphism observed in PAH.

Toward an improved definition of a healthy microbiome for healthy aging

The gut microbiome is a modifier of disease risk because it interacts with nutrition, metabolism, immunity and infection. Aging-related health loss has been correlated with transition to different microbiome states. Microbiome summary indices including alpha diversity are apparently useful to describe these states but belie taxonomic differences that determine biological importance. We analyzed 21,000 fecal microbiomes from seven data repositories, across five continents spanning participant ages 18–107 years, revealing that microbiome diversity and uniqueness correlate with aging, but not healthy aging. Among summary statistics tested, only Kendall uniqueness accurately reflects loss of the core microbiome and the abundance and ranking of disease-associated and health-associated taxa. Increased abundance of these disease-associated taxa and depletion of a coabundant subset of health-associated taxa are a generic feature of aging. These alterations are stronger correlates of unhealthy aging than most microbiome summary statistics and thus help identify better targets for therapeutic modulation of the microbiome.

A Review of the Ecological and Biogeographic Differences of Amazonian Floodplain Forests

Amazonian floodplain forests along large rivers consist of two distinct floras that are traced to their differentiated sediment- and nutrient-rich (várzea) or sediment- and nutrient-poor (igapó) environments. While tree species in both ecosystems have adapted to seasonal floods that may last up to 270–300 days year−1, ecosystem fertility, hydrogeomorphic disturbance regimes, water shortage and drought, fire, and even specific microclimates are distinct between both ecosystems and largely explain the differences in forest productivity and taxonomic composition and diversity. Here, we review existing knowledge about the influence of these environmental factors on the tree flora of both ecosystems, compare species composition and diversity between central Amazonian várzeas and igapós, and show that both ecosystems track distinct species life-history traits. The ecosystem-level and taxonomic differences also largely explain the biogeographic connections of várzeas and igapós to other Amazonian and extra-Amazonian ecosystems. We highlight the major evolutionary force of large-river wetlands for Amazonian tree diversity and explore the scenarios by which the large number of Amazonian floodplain specialist tree species might even contribute to the gamma diversity of the Amazon by generating new species. Finally, we call attention to the urgent need of an improved conservation of Amazonian várzea and igapó ecosystems and their tree species.

Stimulation role of pollen grains in the initial development of Botrytis cinerea: The importance of host compatibility, cultivation status and pollen size

AbstractPlant pollens and fungal spores are massively produced in natural habitats and large‐scaled agricultural areas, and the airborne transported biomass can be accumulated on relatively large crop surfaces. A pollen grain contains a specific chemical composition in quantity and quality, highly varied among plant species. So, the accumulated pollens could provide a species‐specific nutrient supply for the initial fungal development in a pollen trap. Thus, this could increase the variation of the pathogen infection risk in certain plants due to selection mechanisms such as host–pathogen coevolution, crop breeding or pollination type. However, the role of the pollen‐stimulated spore germination and the species‐specific differences in the pollen‐spore interferences is still less understood. Therefore, we performed a multispecies experimental comparison (including 20 plant species) to test the role of the taxon‐specific attributes (i.e. host–pathogen compatibility, cultivation, pollination type and pollen size) in the dose and temporal response of the spore germination in Botrytis cinerea. We found a strong pollen‐stimulating effect on spore germination; however, the triggering effect highly varied among plant species and differed between specific functional categories across temporal and concentration gradients. Specifically, the B. cinerea hosts, the non‐cultivated plants and species with larger pollen size, increased the spore germination's stimulation effects, but not the pollination type. The systematic taxonomic and functional differences might reflect indirectly the diversity of the pollens' chemical profile (i.e. composition matrix or specific trigger molecules) which different selection mechanisms might shape. In the crop–pathogen interactions, the pollen‐stimulation effect could play an essential role in early fungal development.

Smoking by altering the peri-implant microbial community structure compromises the responsiveness to treatment.

Smoking is an essential risk factor for peri-implant diseases. It also hampers the clinical outcomes of peri-implant therapies. Nonetheless, the effect of smoking can go undetected until the emergence of clinical signs. Bacterial-induced inflammation is responsible for the initiation and progression of peri-implant diseases. We hypothesize that smoking impacts the peri-implant microbiome even in status of clinical health, putting it into a sub-healthy condition that responds poorly to peri-implant treatments. To validate this, peri-implant plaque samples from 18 participants including 10 smokers (S) and 8 non-smokers (NS), who had received implant prostheses were analyzed using metagenomic shotgun sequencing. The results showed that in addition to taxonomical and functional differences, the local stability in the S group was also shown to be much higher than that in the NS group, indicating greater stubbornness of the peri-implant microbiome associated with smoking. Besides, the topological structures were also distinct between the two groups. The highly connected species interacted more preferentially with each other in the S group (eigenvector centralization, 0.0273 in S and 0.0183 in NS), resulting in a greater tendency of forming small-world modules (modularity, 0.714 in S and 0.582 in NS). While in the NS group, inter-species correlations were more evenly distributed (clustering coefficient, 0.532 in S and 0.666 in NS). These alterations overall explained the greater stubbornness of the peri-implant microbiome associated with smoking, which may cause poor responsiveness to peri-implant therapies. From a microbial perspective, this may be a potential reason why smoking impacts negatively on the outcome of peri-implant treatments.

Gut microbiota distinct between colorectal cancers with deficient and proficient mismatch repair: A study of 230 CRC patients.

Colorectal cancers (CRCs) with deficient DNA mismatch repair (dMMR) and proficient DNA mismatch repair (pMMR) exhibit heterogeneous tumor characteristics, distinct responses to immunotherapy, and different survival outcomes. However, it is unclear whether gut microbiota is distinct between CRCs with different MMR status. In this study, we used immunohistochemistry for four major MMR proteins to determine the MMR status in 230 CRC patients. The gut microbiota was profiled in cancerous and adjacent normal tissues by using bacterial 16S rRNA sequencing. The differences in microbiota diversity, composition and related metabolic pathways between patients with dMMR and pMMR CRCs were explored. Linear discriminant analysis effect size (LEfSe) analysis was further applied to validate the significant taxonomic differences at the genus level. In our study cohort, dMMR status was identified in 29 of 230 (12.61%) tumors. The richness (alpha-diversity) of gut microbiome in dMMR tumor tissue was higher compared with pMMR tumor tissues. The microbial community composition (beta-diversity) between the two groups was significantly different. The dMMR group was enriched considerably for some microbiota, including Fusobacteria, Firmicutes, Verrucomicrobia, and Actinobacteria at the phylum level and Fusobacterium, Akkermansia, Bifidobacterium, Faecalibacterium, Streptococcus, and Prevotella bacteria at the genus level. However, the pMMR group was dominated by Proteobacteria at the phylum level and Serratia, Cupriavidus and Sphingobium at the genus level. Moreover, a wide variety of microbiota associated functional pathways were observed with different MMR status. KEGG pathway analysis indicated a higher abundance of the biosynthesis and metabolic pathways of glycan and nucleotide, cell growth and death pathways, genetic replication and repair pathways in dMMR samples compared with the pMMR group. These findings demonstrate that CRC patients with different MMR status have distinct gut bacterial community richness, compositions and related metabolic pathways, suggesting basis that may explain the effectiveness of immunotherapy in dMMR tumors.

Oral microbiota may predict the presence of esophageal squamous cell carcinoma.

Microbial imbalances have been well elucidated in esophageal adenocarcinoma (EAC), but few studies address the oral microbiota in esophageal squamous cell carcinoma (ESCC). In view of the fact, we aimed to explore the associations of oral microbiota with these patients suffering from ESCC. In our study, a total of 109 individuals were enrolled (control = 53, ESCC = 56). We profiled the microbiota in oral swabs from individuals with control (ConT) and ESCC (ESCCT). 16S rRNA gene sequencing was applied to analyze the microbiome. The α and β diversity differences were tested by Tukey Test and Partial Least Squares Discriminant Analysis (PLS-DA) respectively. Linear discriminant analysis effect size (LEfSe) analysis was performed to assess taxonomic differences between the two groups. Our results showed that the microbial richness and diversity was a slightly higher in ESCCT groups than that in ConT groups. Bacteroidota, Firmicutes, Proteobacteria, Fusobacteria, Actinobacteria and Patescibacteria were the six dominant bacteria of oral flora in the two groups. When compared with control group, increased Fusobacterioa at phylum level, Neisseriaceae at family level and Leptotrichia at genus level were detected. LEfSe analysis indicated a greater abundance of Leptotrichiaceae, Leptotrichia, Fusobacteriales, Fusobacteria and Fusobacteriota in ESCC groups. Our study suggests a potential association between oral microbiome dysbiosis and ESCC and provides insights on a potential screening marker for esophageal cancer.

Fecal microbiome alterations in treatment-naive de novo Parkinson’s disease

Gut microbiota alterations in Parkinson’s disease (PD) have been found in several studies and are suggested to contribute to the pathogenesis of PD. However, previous results could not be adequately adjusted for a potential confounding effect of PD medication and disease duration, as almost all PD participants were already using dopaminergic medication and were included several years after diagnosis. Here, the gut microbiome composition of treatment-naive de novo PD subjects was assessed compared to healthy controls (HC) in two large independent case-control cohorts (n = 136 and 56 PD, n = 85 and 87 HC), using 16S-sequencing of fecal samples. Relevant variables such as technical batches, diet and constipation were assessed for their potential effects. Overall gut microbiome composition differed between PD and HC in both cohorts, suggesting gut microbiome alterations are already present in de novo PD subjects at the time of diagnosis, without the possible confounding effect of dopaminergic medication. Although no differentially abundant taxon could be replicated in both cohorts, multiple short chain fatty acids (SCFA) producing taxa were decreased in PD in both cohorts. In particular, several taxa belonging to the family Lachnospiraceae were decreased in abundance. Fewer taxonomic differences were found compared to previous studies, indicating smaller effect sizes in de novo PD.

Longitudinal disease-associated gut microbiome differences in infants with food protein-induced allergic proctocolitis

BackgroundComplex interactions between the gut microbiome and immune cells in infancy are thought to be part of the pathogenesis for the marked rise in pediatric allergic diseases, particularly food allergies. Food protein-induced allergic proctocolitis (FPIAP) is commonly the earliest recognized non-immunoglobulin E (IgE)-mediated food allergy in infancy and is associated with atopic dermatitis and subsequent IgE-mediated food allergy later in childhood. Yet, a large prospective longitudinal study of the microbiome of infants with FPIAP, including samples prior to symptom onset, has not been done.ResultsHere, we analyzed 954 longitudinal samples from 160 infants in a nested case-control study (81 who developed FPIAP and 79 matched controls) from 1 week to 1 year of age by 16S rRNA ribosomal gene sequencing as part of the Gastrointestinal Microbiome and Allergic Proctocolitis (GMAP) study. We found key differences in the microbiome of infants with FPIAP, most strongly a higher abundance of a genus of Enterobacteriaceae and a lower abundance of a family of Clostridiales during the symptomatic period. We saw some of these significant taxonomic differences even prior to symptom onset. There were no consistent longitudinal differences in richness or stability diversity metrics between infants with FPIAP and healthy controls.ConclusionsThis study is the first to identify differences in the infant gut microbiome in children who develop FPIAP, some even before they develop symptoms, and provides a foundation for more mechanistic investigation into the pathogenesis of FPIAP and subsequent food allergic diseases in childhood.-xZ6ju8fWHHm1JuGutM5rmVideo abstract.