Microbiota Taxonomic Composition Research Articles

Effects of Vegetable and Fruit Juicing on Gut and Oral Microbiome Composition.

In recent years, juicing has often been promoted as a convenient way to increase fruit and vegetable intake, with juice-only diets marketed for digestive cleansing and overall health improvement. However, juicing removes most insoluble fiber, which may diminish the health benefits of whole fruits and vegetables. Lower fiber intake can alter the microbiota, affecting metabolism, immunity, and mental health, though little is known about juicing's specific effects on the microbiota. This study addresses this gap by exploring how juicing impacts gut and oral microbiome composition in an intervention study. Fourteen participants followed one of three diets-exclusive juice, juice plus food, or plant-based food-for three days. Microbiota samples (stool, saliva, and inner cheek swabs) were collected at baseline, after a pre-intervention elimination diet, immediately after juice intervention, and 14 days after intervention. Moreover, 16S rRNA gene amplicon sequencing was used to analyze microbiota taxonomic composition. The saliva microbiome differed significantly in response to the elimination diet (unweighted UniFrac: F = 1.72, R = 0.06, p < 0.005; weighted UniFrac: F = 7.62, R = 0.23, p-value = 0.0025) with a significant reduction in Firmicutes (p = 0.004) and a significant increase in Proteobacteria (p = 0.005). The juice intervention diets were also associated with changes in the saliva and cheek microbiota, particularly in the relative abundances of pro-inflammatory bacterial families, potentially due to the high sugar and low fiber intake of the juice-related products. Although no significant shifts in overall gut microbiota composition were observed, with either the elimination diet or the juice intervention diets, bacterial taxa associated with gut permeability, inflammation, and cognitive decline increased in relative abundance. These findings suggest that short-term juice consumption may negatively affect the microbiota.

Features of intestinal microbiota taxonomic composition and their relation with hormonal and immune status assessed in women with external genital endometriosis

Aim: systemically assessed characteristics of intestinal microbiota taxonomic composition in relation to parameters of hormonal and immune status in patients with external genital endometriosis (EGE).Materials and Methods. The controlled cross-sectional study included 33 patients with ЕGE comprising main group, and 30 healthy women enrolled to control group. All women underwent assessment of hormonal status and cytokine expression levels in peripheral blood. Level of blood hormones estradiol (E2), follicle-stimulating hormone (FSH), luteinizing hormone (LH), prolactin (PRL) was carried out using enzyme-linked immunosorbent and chemiluminescent assays. Expression levels of cytokines such as interleukin (IL) IL-6, IL-8, tumor necrosis factor alpha (TNF-α) were analyzed by an enzyme-linked immunosorbent assay. Taxonomic composition of intestinal microbiota at the level of phyla and genera was carried out by 16S ribosomal RNA genesequencing. Microbial community α-diversity, the Chao1, ACE, and Sobs indices were used.Results. The concentration of blood E2 in main group was significantly higher compared to control group. Also, women with ЕGE had higher plasma concentrations for IL-6, IL-8, IL-17 and TNF-α compared to those in control group (p &lt; 0.001). While analyzing bacterial community α-diversity in main group, Chao1 index was found to be significantly decreased. At the phylum level, the Firmicutes/Bacteroidetes ratio was increased in patients with ЕGE compared with that in control group. Among the 20 largest genera in patients with ЕGE, significant abundance was observed for Lachnospira, Blautia, Dorea, Streptococcus, Eubacterium hallii_group paralleled with significant decline in Bifidobacterium and Eubacterium eligens_group. A positive correlation was obtained between estrogen levels and the number of representatives from the genera Eubacterium hallii_group and Streptococcus, IL-8 and Streptococcus, TNF-α and Streptococcus and Lachnospira, as well as a negative correlation between TNF-α and Bifidobacterium.Conclusion. A relation between dysbiotic intestinal alterations and developing endometriosis was found. The identified correlations between altered taxonomic composition of the intestinal microflora and parameters of hormonal and immune status in patients with ЕGE suggest that intestinal microbiota is involved in pathophysiology of endometriosis.

Diet-induced changes in the jejunal microbiota of developing broilers reduce the abundance of Enterococcus hirae and Enterococcus faecium

Modern broiler breeds allow for high feed efficiency and rapid growth, which come at a cost of increased susceptibility to pathogens and disease. Broiler growth rate, feed efficiency, and health are affected by the composition of the gut microbiota, which in turn is influenced by diet. In this study, we therefore assessed how diet composition can affect the broiler jejunal gut microbiota. A total of 96 broiler chickens were divided into four diet groups: control, coated butyrate supplementation, medium-chain fatty acid supplementation, or a high-fibre low-protein content. Diet groups were sub-divided into age groups (4, 12 and 33 days of age) resulting in groups of 8 broilers per diet per age. The jejunum content was used for metagenomic shotgun sequencing to determine the microbiota taxonomic composition at species level. The composed diets resulted in a total of 104 differentially abundant bacterial species. Most notably were the butyrate-induced changes in the jejunal microbiota of broilers 4 days post-hatch, resulting in the reduced relative abundance of mainly Enterococcus faecium (-1.8 l2fc, Padj = 9.9E-05) and the opportunistic pathogen Enterococcus hirae (-2.9 l2fc, Padj = 2.7E-08), when compared to the control diet. This effect takes place during early broiler development, which is critical for broiler health, thus exemplifying the importance of how diet can influence the microbiota composition in relation to broiler health. Future studies should therefore elucidate how diet can be used to promote a beneficial microbiota in the early stages of broiler development.

Microbiota is structured by gut regions, life stage, and diet in the Black Soldier Fly (Hermetia illucens).

The larvae of the Black Soldier Fly (Hermetia illucens) provide numerous ecological benefits, leading to significant commercial advancements. These benefits include the bioconversion of low-value waste into high-value feed and soil amendments. Understanding how the bacterial and eukaryotic microbiota communities affect host performance becomes vital for the optimization and specialization of industrial-scale rearing. This study investigates H. illucens-associated microbiota taxonomic composition and dynamics across the developmental cycle (eggs, neonates, larvae, prepupae, and imago X0 to second generation X1) when reared on two substrates: (i) plant-based (Housefly Gainesville diet) and (ii) animal-based (poultry hatchery waste). By using the 16S gene amplicon metataxonomic approach, we found that the results revealed that bacterial microbiota inherited from parents reared on a different substrate may have induced dysbiosis in the progeny. Specifically, the interaction networks of individuals reared on hatchery waste showed a high prevalence of negative interactions and low connectivity. Proteobacteria (39-92%), Firmicutes (4-39%), Bacteroidota (1-38%), and Actinobacteria (1-33%). In animal feed-reared individuals, Firmicutes reached the highest relative abundance (10-80%), followed by Proteobacteria (6-55%), Actinobacteria (1-31%), and Bacteroidota (0-22%). The rearing substrate was the main driver of microbiota composition, while the developmental stage influenced only the whole individual's bacterial microbiota composition. Gut regions were associated with distinct bacterial composition and richness, with diversity decreasing along the digestive tract. For the first time, microeukaryotes of the microbiota other than Fungi were investigated using 18S genetic marker amplicon sequencing with novel blocking primers specific to the Black Soldier Fly. Microeukaryotes are a neglected part of multitrophic microbiota communities that can have similar effects on their hosts as bacterial microbiota. Microeukaryotes from seven orders were identified in black soldier flies, including potential pathogens (e.g., Aplicomplexa group). Nucletmycea were the dominant class throughout development, followed by Holozoa and Stramenophiles. The eukaryote microbiota was structured by developmental stages but not by gut regions. Insights from this study are a stepping stone toward the microbiological optimization of black soldier flies for industrial rearing, highlighting how a synthetic microbiota assembly should be tailored to the rearing environment of the larvae at a targeted developmental stage.

Low dose dietary contamination with deoxynivalenol mycotoxin exacerbates enteritis and colorectal cancer in mice

Low dose dietary contamination with deoxynivalenol mycotoxin exacerbates enteritis and colorectal cancer in mice

Изменения микробиоты кишечника и их связь с показателями IL6, IL8 и TNFα у пациенток с наружным генитальным эндометриозом

Today, the association of gut microbiota with external genital endometriosis (EGE) is of special scientific interest. The study was aimed to assess alterations of the gut microbiota taxonomic composition and explore their correlations with plasma levels of IL6, IL8 and TNFα at the species level in patients with EGE. The crosssectional comparative study involved 50 patients with EGE (index group) and 50 healthy women (control group). The changes in the gut microbiota taxonomic composition and plasma levels of IL6, IL8 and TNFα were assessed. A significant decrease in the abundance of such species, as Coprococcus catu (р = 0.009), Turicibacter sanguinis (р = 0.008) and Ruminococcus gnavus (р &lt; 0.001), along with the increase in the abundance of Eubacterium ramulus (р = 0.040), Bacterioides dorei (р = 0.001), Prevotella divia (р = 0.008) and Shigella flexneri (р &lt; 0.001) were found in the gut microbiota taxonomic composition in patients with EGE. Significant correlations between the IL6 levels and the abundance of Turicibacter sanguinis (r = –0.92; р = 0.001), IL8 levels and the abundance of Shigella flexneri (r = 0.72; р &lt; 0.001), TNFα levels and the abundance of Prevotella divia (r = 0.77; р = 0.001) were revealed. The findings add to the available literature data on the features of gut microbiota alterations and their association with some inflammation biomarkers in individuals with EGE, which can justify further research in this area and probably open up new approaches to treatment of the disease.

The fecal microbiotas of women of Pacific and New Zealand European ethnicities are characterized by distinctive enterotypes that reflect dietary intakes and fecal water content

ABSTRACT Obesity is a complex, multifactorial condition that is an important risk factor for noncommunicable diseases including cardiovascular disease and type 2 diabetes. While prevention and management require a healthy and energy balanced diet and adequate physical activity, the taxonomic composition and functional attributes of the colonic microbiota may have a supplementary role in the development of obesity. The taxonomic composition and metabolic capacity of the fecal microbiota of 286 women, resident in Auckland New Zealand, was determined by metagenomic analysis. Associations with BMI (obese, nonobese), body fat composition, and ethnicity (Pacific, n = 125; NZ European women [NZE], n = 161) were assessed using regression analyses. The fecal microbiotas were characterized by the presence of three distinctive enterotypes, with enterotype 1 represented in both Pacific and NZE women (39 and 61%, respectively), enterotype 2 mainly in Pacific women (84 and 16%) and enterotype 3 mainly in NZE women (13 and 87%). Enterotype 1 was characterized mainly by the relative abundances of butyrate producing species, Eubacterium rectale and Faecalibacterium prausnitzii, enterotype 2 by the relative abundances of lactic acid producing species, Bifidobacterium adolescentis, Bifidobacterium bifidum, and Lactobacillus ruminis, and enterotype 3 by the relative abundances of Subdoligranulum sp., Akkermansia muciniphila, Ruminococcus bromii, and Methanobrevibacter smithii. Enterotypes were also associated with BMI, visceral fat %, and blood cholesterol. Habitual food group intake was estimated using a 5 day nonconsecutive estimated food record and a 30 day, 220 item semi-quantitative Food Frequency Questionnaire. Higher intake of ‘egg’ and ‘dairy’ products was associated with enterotype 3, whereas ‘non-starchy vegetables’, ‘nuts and seeds’ and ‘plant-based fats’ were positively associated with enterotype 1. In contrast, these same food groups were inversely associated with enterotype 2. Fecal water content, as a proxy for stool consistency/colonic transit time, was associated with microbiota taxonomic composition and gene pools reflective of particular bacterial biochemical pathways. The fecal microbiotas of women of Pacific and New Zealand European ethnicities are characterized by distinctive enterotypes, most likely due to differential dietary intake and fecal consistency/colonic transit time. These parameters need to be considered in future analyses of human fecal microbiotas.

Изменения микробиоты кишечника у больных ювенильным идиопатическим артритом

Currently, the issue of the relationship between gut microbiota and juvenile idiopathic arthritis (JIA) is still relevant. The study was aimed to assess alterations in the gut microbiota taxonomic composition and estimate the relationship between these alterations and cortisol, melatonin, and TNFα at the genus level in patients with JIA. The comparative cross-sectional study involved 65 patients with JIA (index group) and 60 healthy children (control group). The gut microbiota taxonomic composition and plasma levels of cortisol, melatonin, and TNFα were assessed. The following alterations of the gut microbiota taxonomic composition were found in patients with JIA: the significantly decreased abundance of Anaerostipes (р = 0.042), Lachnospira (р = 0.034), Roseburia (р = 0.002), Coprococcus (р = 0.014), Dialister (р = 0.003) and the increase in the abundance of Ruminococcus (р = 0.012). There were significant correlations of cortisol levels with the abundance of Lachnospira (r = –0.44; p = 0.001), melatonin concentrations and the abundance of Coprococcus (r = –0.48; p = 0.023), the levels of TNFα and the abundance of Ruminococcus (r = 0.52; p = 0.001). The association of the Lachnospira, Roseburia, and Ruminococcus abundance with the higher DAS28 scores was discovered (r = –0.57; p = 0.002; r = –0.44; p = 0.002; r = 0.54; p = 0.032, respectively). The findings provide additional information about the features of gut microbiota alterations and their correlation with some hormone and inflammatory biomarkers associated with JIA, that could provide the basis for further research and possibly for new approaches to treatment of this disorder.

Combination effect between gut microbiota and traditional potentially modifiable risk factors for first-ever ischemic stroke in Tujia, Miao and Han populations in China.

China has had explosive growth in ischemic stroke (IS) burden with significant ethnic and geographic disparities. The aim of this study was to explore the possible combination effect between gut microbiota and traditional potentially modifiable risk factors for IS among two ethnic minorities (Tujia and Miao) and the Han population. Herein, we first used the 16 S rRNA sequencing to compare the gut microbial compositions of 82 patients with first-ever IS vs. 82 normal controls (NCs) among Han, Tujia, and Miao people between 1 May 2018 and 30 April 2019, from Xiangxi Tujia and Miao Autonomous Prefecture in China. An additive model was used to study the interaction between traditional risk factors and gut microbiota with R software. Linear discriminant analysis (LDA) and LDA effect size (LEfSe) results showed that the identified key gut microbiota's taxonomic composition varied in different ethnicity between the IS patients and NCs. Furthermore, families Lactobacillaceae, Enterococcaceae, Streptococcaceae, and Enterobacteriaceae were found to be positively correlated with high-risk factors and negatively correlated with preventive factors in the IS patients, but families Ruminococcaceae and Lachnospiraceae were just the opposite in the NCs. There were additive interactions between traditional risk factors (systolic blood pressure, diastolic blood pressure, and high-sensitive C-reactive protein) and family Enterococcaceae for first-ever IS with the attributable proportion due to the interaction was 0.74, 0.71, and 0.85, respectively; and the synergy index was 4.45, 3.78, and 7.01, respectively. This preliminary but promising study showed that the gut microbiota disturbances may potentially interact to IS with different ethnic host's traditional risk factors.

The association between fecal microbiota, age and endoparasitism in adult alpacas.

Endoparasitism is a major cause of morbidity and mortality in alpacas (Lama pacos), with growing emergence of anthelmintic resistance. The purpose of the study was to correlate nematode worm burden and selected host phenotypic characteristics, such as age and weight, with the composition of the intestinal microbiota of adult alpacas. Fecal samples were collected per rectum from 102 healthy adult (2.1–11.2 years) alpacas at 3 separate timepoints (pre- and post-treatment with 8.8 mg/kg oral Levamisole HCL, and 4.6 months later) at a single farm. The profile of the fecal bacterial microbiota was characterized using 16S amplicon sequencing. Serial clinical exams and fecal egg counts were compared using related-samples analyses. The fecal microbiota of identically managed, healthy alpacas was characterized by a high level of temporal stability, as both α and β-diversity significantly correlated between sampling timepoints. Pairwise β-diversity between samples collected at each timepoint was low, ranging from 0.16–0.21 UniFrac distance units. The intensity of strongylid nematode infection (including Haemonchus, Ostertagia, Trichostrongylus) was only significantly correlated with microbiota composition in samples collected 14 days after treatment with levamisole. Analysis of similarity revealed no clustering of microbiota from anthelmintic responders or non-responders. Alpaca age explained the largest proportion of fecal microbiota variation and was the only consistently significant predictor of fecal microbiota taxonomic composition, by impacting the ratio of relative Bacteroidetes and Firmicutes abundance. Firmicutes, mostly Clostridiales, was the most abundant taxon across all collections.

Changes in fish skin microbiota along gradients of eutrophication in human-altered rivers.

Changes in fish skin microbiota along gradients of eutrophication in human-altered rivers.

Differences in caecal microbiota composition and Salmonella carriage between experimentally infected inbred lines of chickens

BackgroundSalmonella Enteritidis (SE) is one of the major causes of human foodborne intoxication resulting from consumption of contaminated poultry products. Genetic selection of animals that are more resistant to Salmonella carriage and modulation of the gut microbiota are two promising ways to decrease individual Salmonella carriage. The aims of this study were to identify the main genetic and microbial factors that control the level of Salmonella carriage in chickens (Gallus gallus) under controlled experimental conditions. Two-hundred and forty animals from the White Leghorn inbred lines N and 61 were infected by SE at 7 days of age. After infection, animals were kept in isolators to reduce recontamination of birds by Salmonella. Caecal contents were sampled at 12 days post-infection and used for DNA extraction. Microbiota DNA was used to measure individual counts of SE by digital PCR and to determine the bacterial taxonomic composition, using a 16S rRNA gene high-throughput sequencing approach.ResultsOur results confirmed that the N line is more resistant to Salmonella carriage than the 61 line, and that intra-line variability is higher for the 61 line. Furthermore, the 16S analysis showed strong significant differences in microbiota taxonomic composition between the two lines. Among the 617 operational taxonomic units (OTU) observed, more than 390 were differentially abundant between the two lines. Furthermore, within the 61 line, we found a difference in the microbiota taxonomic composition between the high and low Salmonella carriers, with 39 differentially abundant OTU. Using metagenome functional prediction based on 16S data, several metabolic pathways that are potentially associated to microbiota taxonomic differences (e.g. short chain fatty acids pathways) were identified between high and low carriers.ConclusionsOverall, our findings demonstrate that the caecal microbiota composition differs between genetic lines of chickens. This could be one of the reasons why the investigated lines differed in Salmonella carriage levels under experimental infection conditions.

Structural changes in the gut microbiota community of the black-necked crane (Grus nigricollis) in the wintering period.

During overwintering of black-necked cranes (Grus nigricollis), the composition and function of the gut microbiota changes are of considerable interest for understanding its environmental adaption mechanism. In this study, we characterized the structure of the gut microbiota from the black-necked crane in the Dashanbao wintering area, and compared the early-winter (November) microbiota to the late-winter (March of the next year) microbiota. The results showed that the gut microbiota diversity of black-necked crane in the early-overwintering stage was higher than that in the late-overwintering stage, but it did not reach a significant level. Gut microbiota taxonomic composition analysis showed that relative abundance of Bacteroidota increased significantly, and showed decreased Firmicutes to Bacteroidota ratio at the phylum level, meanwhile, the abundance of Lactobacillus decreased significantly at the genus level. Explain gut microbiota between the early- and late-wintering showed some differences in microbiota richness but maintained a relatively conservative microbiota structure. PICRUSt2 method was used to predict and analyze the KEGG functional abundance of 16S rDNA sequences of bacteria, it was found that the changes in gut microbiota composition increased the abundance of bacteria associated with amino acid biosynthesis and acid metabolism in the late stage of overwintering. This work provides basic data for black-necked crane gut microbiota study, which might further contribute to their protection.

Effects of deoxynivalenol-contaminated diet on the composition and diversity of the intestinal microbial community and intestinal ultrastructure of juvenile largemouth bass (Micropterus salmoides)

Effects of deoxynivalenol-contaminated diet on the composition and diversity of the intestinal microbial community and intestinal ultrastructure of juvenile largemouth bass (Micropterus salmoides)

Microbiota restoration reduces antibiotic-resistant bacteria gut colonization in patients with recurrent Clostridioides difficile infection from the open-label PUNCH CD study

BackgroundOnce antibiotic-resistant bacteria become established within the gut microbiota, they can cause infections in the host and be transmitted to other people and the environment. Currently, there are no effective modalities for decreasing or preventing colonization by antibiotic-resistant bacteria. Intestinal microbiota restoration can prevent Clostridioides difficile infection (CDI) recurrences. Another potential application of microbiota restoration is suppression of non-C. difficile multidrug-resistant bacteria and overall decrease in the abundance of antibiotic resistance genes (the resistome) within the gut microbiota. This study characterizes the effects of RBX2660, a microbiota-based investigational therapeutic, on the composition and abundance of the gut microbiota and resistome, as well as multidrug-resistant organism carriage, after delivery to patients suffering from recurrent CDI.MethodsAn open-label, multi-center clinical trial in 11 centers in the USA for the safety and efficacy of RBX2660 on recurrent CDI was conducted. Fecal specimens from 29 of these subjects with recurrent CDI who received either one (N = 16) or two doses of RBX2660 (N = 13) were analyzed secondarily. Stool samples were collected prior to and at intervals up to 6 months post-therapy and analyzed in three ways: (1) 16S rRNA gene sequencing for microbiota taxonomic composition, (2) whole metagenome shotgun sequencing for functional pathways and antibiotic resistome content, and (3) selective and differential bacterial culturing followed by isolate genome sequencing to longitudinally track multidrug-resistant organisms.ResultsSuccessful prevention of CDI recurrence with RBX2660 correlated with taxonomic convergence of patient microbiota to the donor microbiota as measured by weighted UniFrac distance. RBX2660 dramatically reduced the abundance of antibiotic-resistant Enterobacteriaceae in the 2 months after administration. Fecal antibiotic resistance gene carriage decreased in direct relationship to the degree to which donor microbiota engrafted.ConclusionsMicrobiota-based therapeutics reduce resistance gene abundance and resistant organisms in the recipient gut microbiome. This approach could potentially reduce the risk of infections caused by resistant organisms within the patient and the transfer of resistance genes or pathogens to others.Trial registrationClinicalTrials.gov, NCT01925417; registered on August 19, 2013.

Gut Microbiota Dysbiosis and Elevated Lipopolysaccharide Serum Levels Are Associated with Venous Thromboembolism in Pediatric Patients

Gut Microbiota Dysbiosis and Elevated Lipopolysaccharide Serum Levels Are Associated with Venous Thromboembolism in Pediatric Patients

Dynamics of the Honeybee (Apis mellifera) Gut Microbiota Throughout the Overwintering Period in Canada.

Microbial symbionts inhabiting the honeybee gut (i.e., gut microbiota) are essential for food digestion, immunity, and gut protection of their host. The taxonomic composition of the gut microbiota is dynamic throughout the honeybee life cycle and the foraging season. However, it remains unclear how drastic changes occurring in winter, such as food shortage and cold weather, impact gut microbiota dynamics. The objective of this study was to characterize the gut microbiota of the honeybee during the overwintering period in a northern temperate climate in Canada. The microbiota of nine honeybee colonies was characterized by metataxonomy of 16S rDNA between September 2017 and June 2018. Overall, the results showed that microbiota taxonomic composition experienced major compositional shifts in fall and spring. From September to November, Enterobacteriaceae decreased, while Neisseriaceae increased. From April to June, Orbaceae increased, whereas Rhizobiaceae nearly disappeared. Bacterial diversity of the gut microbiota decreased drastically before and after overwintering, but it remained stable during winter. We conclude that the honeybee gut microbiota is likely to be impacted by the important meteorological and dietary changes that take place before and after the overwintering period. Laboratory trials are needed to determine how the observed variations affect the honeybee health.

Broilers divergently selected for digestibility differ for their digestive microbial ecosystems.

Improving the digestive efficiency of broiler chickens (Gallus gallus) could reduce organic waste, increase the use of alternative feed not used for human consumption and reduce the impact of feed in production costs. By selecting chicken lines divergently for their digestive efficiency, we showed previously that digestive efficiency is under genetic control and that the two resulting divergent lines, D+ (high digestive efficiency or “digestibility +”) and D- (low digestive efficiency or “digestibility -”), also differ for the abundance of specific bacteria in their caeca. Here we perform a more extensive census of the bacteria present in the digestive microbiota of 60 chickens selected for their low apparent metabolizable energy corrected for nitrogen balance (AMEn-) or high (AMEn+) digestive efficiency in a [D+ x D-] F8 progeny of 200 individuals. We sequenced the 16S rRNA genes of the ileal, jejunal and caecal microbiotas, and compared the compositions and predicted functions of microbiotas from the different intestinal segments for 20 AMEn+ and 19 AMEn- birds. The intestinal segment of origin was the main factor structuring the samples. The caecal microbiota was the most impacted by the differences in digestive efficiency, with 41 bacterial species with abundances differing between highly and poorly efficient birds. Furthermore, we predicted that the caecal microbiota of efficient birds might be enriched in genes contributing to the degradation of short chain fatty acids (SCFA) from non-starch polysaccharides. These results confirm the impact of the genetic selection led on digestibility on the caecal microbiota taxonomic composition. They open the way toward the identification of specific, causal genes of the host controlling variations in the abundances of bacterial taxons.

Diagnostic potential of gut microbiota in Parkinson’s disease

Background. Nowadays many efforts are taken in searching for Parkinson’s disease biomarkers, especially for an early recognition of the disease. The gut microbiota is one of the potential sources of biomarkers, changes in the composition of which in PD are actively studied.The aim of this study is to identify microbiota biomarkers in the Parkinson’s disease with an estimated accuracy of the diagnostics, including differential diagnostics, relative to other neurological diseases for patients of the Russian population.Material and methods. One hundred ninety-two metagenomics profiles from patients with Parkinson’s disease (n = 93), people with other neurological diagnoses (n = 33), and healthy controls (n = 66) were included in this study. These profiles were obtained with amplicon sequencing of bacterial 16S rRNA genes. Classifying models were made using the naive Bayes classifier, the artificial neural network, support vector machine, generalized linear model, and partial least squares regression.As a result we established that an optimal classification by the composition of the gut microbiota on the validation sample (sensitivity 91.30%, specificity 91.67% at 91.49% accuracy) amid patients was demonstrated with a naive Bayes classifier using the representation of the following genera as predictors: Christensenella, Methanobrevibacter, Leuconostoc, Enterococcus, Catabacter, Desulfovibrio, Sphingomonas, Yokenella, Atopobium, Fusicatenibacter, Cloacibacillus, Bulleidia, Acetanaerobacterium, and Staphylococcus.Conclusions. Information of the gut microbiota taxonomic composition may be used in differential diagnosis of Parkinson’s disease.

Super-dominant pathobiontic bacteria in the nasopharyngeal microbiota as causative agents of secondary bacterial infection in influenza patients

ABSTRACT The source of secondary lower respiratory tract bacterial infections in influenza patients is not fully understood. A case–control study was conducted during the 2017–2018 influenza epidemic period in Beijing, China. Nasopharyngeal swabs were collected from 52 virologically confirmed influenza patients and 24 healthy medical staff. The nasopharyngeal microbiota taxonomic composition was analysed using high-throughput sequencing of the 16S rRNA gene V3–V4 regions. The super-dominant pathobiontic bacterial genus (SDPG) was defined as that accounting for >50% of sequences in a nasopharyngeal swab. We attempted to isolate bacteria of this genus from both nasopharyngeal swabs and lower-respiratory tract samples and analyse their genetic similarities. We observed a significantly lower taxonomy richness in influenza cases compared with healthy controls. A SDPG was detected in 61% of severe cases but in only 24% of mild cases and 29% of healthy controls. In 10 cases, the species isolated from lower-respiratory tract infection sites were identified as belonging to the nasopharyngeal microbiota SDPG. Genetically identical strains were isolated from both nasopharyngeal swabs and lower-respiratory tract infection sites, including 23 Acinetobacter baumannii strains from six severe cases, six Klebsiella pneumoniae strains from two severe cases, five Pseudomonas aeruginosa strains from one severe and one mild case, and four Corynebacterium striatum strains from two severe cases. The SDPG in the nasopharyngeal microbiota are the likely cause of subsequent infection in influenza patients.