Comparing the anterior nare bacterial community of two discrete human populations using Illumina amplicon sequencing

Portulaca oleracea exhibited anti-coccidian activity, fortified the gut microbiota of Hu lambs

Coccidia of the genus Eimeria are important pathogens that cause coccidiosis in livestock and poultry. Due to the expansion of intensive farming, coccidiosis has become more difficult to control. In addition, the continued use of anti-coccidiosis drugs has led to drug resistance and residue. Some herbs used in traditional Chinese medicine (TCM) have been shown to alleviate the clinical symptoms of coccidiosis, while enhancing immunity and growth performance (GP) of livestock and poultry. Previous in vitro and in vivo studies have reported that the TCM herb Portulaca oleracea exhibited anti-parasitic activities. In total, 36 female Hu lambs were equally divided into six treatment groups: PL (low-dose P. oleracea), PH (high-dose P. oleracea), PW (P. oleracea water extract), PE (P. oleracea ethanol extract), DIC (diclazuril), and CON (control). The treatment period was 14 days. The McMaster counting method was used to evaluate the anti-coccidiosis effects of the different treatments. Untargeted metabolomics and 16S rRNA gene sequencing were used to investigate the effects of treatment on the gut microbiota (GM) and GP. The results showed that P. oleracea ameliorated coccidiosis, improved GP, increased the abundances of beneficial bacteria, and maintained the composition of the GM, but failed to completely clear coccidian oocysts. The Firmicutes to Bacteroides ratio was significantly increased in the PH group. P. oleracea increased metabolism of tryptophan as well as some vitamins and cofactors in the GM and decreased the relative content of arginine, tryptophan, niacin, and other nutrients, thereby promoting intestinal health and enhancing GP. As an alternative to the anti-coccidiosis drug DIC, P. oleracea effectively inhibited growth of coccidia, maintained the composition of the GM, promoted intestinal health, and increased nutrient digestibility.

Cell-Free Microbial DNA Analysis: Effects of Blood Plasma and Serum Quantity, Biobanking Protocols, and Isolation Kits

Recent studies highlight the presence of bacterial sequences in the human blood, suggesting potential clinical significance for circulating microbial signatures. These sequences could presumably serve in the diagnosis, prediction, or monitoring of various health conditions. Ensuring the similarity of samples before bacterial analysis is crucial, especially when combining samples from different biobanks prepared under varying conditions (such as different DNA extraction kits, centrifugation conditions, blood collection tubes, etc.). In this study, we aimed to analyze the impact of different sample collection and nucleic acid extraction criteria (blood collection tube, centrifugation, input volume, and DNA extraction kit) on circulating bacterial composition. Blood samples from four healthy individuals were collected into three different sample collection tubes: K2EDTA plasma tube, sodium citrate plasma tube, and gel tube for blood serum. Tubes were centrifugated at standard and double centrifugation conditions. DNA extraction was performed using 100, 200, and 500 μL plasma/serum input volumes. DNA extraction was performed using three different isolation kits: Norgen plasma/serum cell-free circulating DNA purification micro kit, Applied Biosystems MagMAX cell-free DNA isolation kit, and Qiagen QIAamp MinElute cell-free circulating DNA mini kit. All samples were subjected to 16S rRNA V1-V2 library preparation and sequencing. In total, 216 DNA and 18 water control samples were included in the study. According to PERMANOVA, PCoA, Mann-Whitney, and FDR tests the effect of the DNA extraction kit on the microbiota composition was the greatest, whereas the type of blood collection tube, centrifugation type, and sample input volume for the extraction had minor effects. Samples extracted with the Norgen DNA extraction kit were enriched with Gram-negative bacteria, whereas samples extracted with the Qiagen and MagMAX kits were enriched with Gram-positive bacteria. Bacterial profiles of samples prepared with the Qiagen and MagMAX DNA extraction kits were more similar, whereas samples prepared with the Norgen DNA extraction kit were significantly different from other groups.

The colibactin-producing Escherichia coli alters the tumor microenvironment to immunosuppressive lipid overload facilitating colorectal cancer progression and chemoresistance

Intratumoral bacteria flexibly contribute to cellular and molecular tumor heterogeneity for supporting cancer recurrence through poorly understood mechanisms. Using spatial metabolomic profiling technologies and 16SrRNA sequencing, we herein report that right-sided colorectal tumors are predominantly populated with Colibactin-producing Escherichia coli (CoPEC) that are locally establishing a high-glycerophospholipid microenvironment with lowered immunogenicity. It coincided with a reduced infiltration of CD8+ T lymphocytes that produce the cytotoxic cytokines IFN-γ where invading bacteria have been geolocated. Mechanistically, the accumulation of lipid droplets in infected cancer cells relied on the production of colibactin as a measure to limit genotoxic stress to some extent. Such heightened phosphatidylcholine remodeling by the enzyme of the Land's cycle supplied CoPEC-infected cancer cells with sufficient energy for sustaining cell survival in response to chemotherapies. This accords with the lowered overall survival of colorectal patients at stage III-IV who were colonized by CoPEC when compared to patients at stage I-II. Accordingly, the sensitivity of CoPEC-infected cancer cells to chemotherapies was restored upon treatment with an acyl-CoA synthetase inhibitor. By contrast, such metabolic dysregulation leading to chemoresistance was not observed in human colon cancer cells that were infected with the mutant strain that did not produce colibactin (11G5∆ClbQ). This work revealed that CoPEC locally supports an energy trade-off lipid overload within tumors for lowering tumor immunogenicity. This may pave the way for improving chemoresistance and subsequently outcome of CRC patients who are colonized by CoPEC.

Host Species and Environment Shape the Gut Microbiota of Cohabiting Marine Bivalves

Pacific oysters (Crassostrea gigas) and Mediterranean mussels (Mytilus galloprovincialis) are commercially important marine bivalves that frequently coexist and have overlapping feeding ecologies. Like other invertebrates, their gut microbiota is thought to play an important role in supporting their health and nutrition. Yet, little is known regarding the role of the host and environment in driving these communities. Here, bacterial assemblages were surveyed from seawater and gut aspirates of farmed C. gigas and co-occurring wild M. galloprovincialis in summer and winter using Illumina 16S rRNA gene sequencing. Unlike seawater, which was dominated by Pseudomonadata, bivalve samples largely consisted of Mycoplasmatota (Mollicutes) and accounted for >50% of the total OTU abundance. Despite large numbers of common (core) bacterial taxa, bivalve-specific species (OTUs) were also evident and predominantly associated with Mycoplasmataceae (notably Mycoplasma). An increase in diversity (though with varied taxonomic evenness) was observed in winter for both bivalves and was associated with changes in the abundance of core and bivalve-specific taxa, including several representing host-associated and environmental (free-living or particle-diet associated) organisms. Our findings highlight the contribution of the environment and the host in defining the composition of the gut microbiota in cohabiting, intergeneric bivalve populations.

Gender-specific changes of the gut microbiome correlate with tumor development in murine models of pancreatic cancer

Pancreatic ductal adenocarcinoma (PDAC) is a devastating disease with a dismal outcome. To improve understanding of sequential microbiome changes during PDAC development we analyzed mouse models of pancreatic carcinogenesis (KC mice recapitulating pre-invasive PanIN formation, as well as KPC mice recapitulating invasive PDAC) during early tumor development and subsequent tumor progression. Diversity and community composition were analyzed depending on genotype, age, and gender. Both mouse models demonstrated concordant abundance changes of several genera influenced by one or more of the investigated factors. Abundance was significantly impacted by gender, highlighting the need to further elucidate the impact of gender differences. The findings underline the importance of the microbiome in PDAC development and indicate that microbiological screening of patients at risk and targeting the microbiome in PDAC development may be feasible in future.

Maternal weight, gut microbiota, and the association with early childhood behavior: the PREOBE follow-up study

BACKGROUND AND AIM

Maternal overweight and breastfeeding seem to have a significant impact on the gut microbiota colonization process, which co-occurs simultaneously with brain development and the establishment of the "microbiota-gut-brain axis", which potentially may affect behavior later in life. This study aimed to examine the influence of maternal overweight, obesity and/or gestational diabetes on the offspring behavior at 3.5 years of age and its association with the gut microbiota already established at 18 months of life.

METHODS

156 children born to overweight (OV, n = 45), obese (OB, n = 40) and normoweight (NW, n = 71) pregnant women participating in the PREOBE study were included in the current analysis. Stool samples were collected at 18 months of life and gut microbiome was obtained by 16S rRNA gene sequencing. Behavioral problems were evaluated at 3.5 years by using the Child Behavior Checklist (CBCL). ANOVA, Chi-Square Test, ANCOVA, Spearman's correlation, logistic regression model and generalized linear model (GLM) were performed.

RESULTS

At 3.5 years of age, Children born to OV/OB mothers showed higher scores in behavioral problems than those born to NW mothers. Additionally, offspring born to OB mothers who developed gestational diabetes mellitus (GDM) presented higher scores in attention/deficit hyperactivity and externalizing problems than those born to GDM OV/NW mothers. Fusicatenibacter abundance found at 18 months of age was associated to lower scores in total, internalizing and pervasive developmental problems, while an unidentified genus within Clostridiales and Flavonifractor families abundance showed a positive correlation with anxiety/depression and somatic complaints, respectively. On the other hand, children born to mothers with higher BMI who were breastfed presented elevated anxiety, internalizing problems, externalizing problems and total problems scores; likewise, their gut microbiota composition at 18 months of age showed positive correlation with behavioral problems at 3.5 years: Actinobacteria abundance and somatic complaints and between Fusobacteria abundance and withdrawn behavior and pervasive developmental problems.

CONCLUSIONS

Our findings suggests that OV/OB and/or GDM during pregnancy is associated with higher behavioral problems scores in children at 3.5 years old. Additionally, associations between early life gut microbiota composition and later mental health in children was also found.

Microbial composition of tumorous and adjacent gastric tissue is associated with prognosis of gastric cancer

Helicobacter pylori (H. pylori) infection has been considered as the main causal factor in gastric carcinogenesis, but other bacterial species may also play an important role in pathophysiology of gastric cancer. The aim of the study was to explore the link between gastric cancer prognosis and the mucosal microbial community in tumorous and adjacent gastric tissue. The bacterial profile was analysed using 16S sequencing (V1-V2 region). Microbial differences were mostly characterized by lower relative abundances of H. pylori in tumorous gastric tissues. Bacterial community and outcome data analysis revealed the genus Fusobacterium and Prevotella significantly associated with worse overall survival in gastric cancer patients. In particular, Fusobacterium was associated with significant increase in hazard ratio in both univariable and multivariable analysis and independently validated using TCMA data. Phylogenetic biodiversity of Fusobacterium species in the stomach revealed F. periodonticum as the most prevalent in healthy subjects, while F. nucleatum was most abundant in patients with gastric cancer. Bacterial community network analysis in gastric cancer suggests substantial complexity and a strong interplay between F. nucleatum and Prevotella. In summary, mucosal microbial community in the stomach was associated with worse overall survival in gastric cancer patients. Strongest negative impact on prognosis was linked to the abundance of F. nucleatum in tumorous specimens, suggesting its translational relevance in management of gastric cancer patients.

Comparison of genomic and transcriptional microbiome analysis in gastric cancer patients and healthy individuals

BACKGROUND

Helicobacter pylori and the stomach microbiome play a crucial role in gastric carcinogenesis, and detailed characterization of the microbiome is necessary for a better understanding of the pathophysiology of the disease. There are two common modalities for microbiome analysis: DNA (16S rRNA gene) and RNA (16S rRNA transcript) sequencing. The implications from the use of one or another sequencing approach on the characterization and comparability of the mucosal microbiome in gastric cancer (GC) are poorly studied.

AIM

To characterize the microbiota of GC using 16S rRNA gene and its transcript and determine difference in the bacterial composition.

METHODS

In this study, 316 DNA and RNA samples extracted from 105 individual stomach biopsies were included. The study cohort consisted of 29 healthy control individuals and 76 patients with GC. Gastric tissue biopsy samples were collected from damaged mucosa and healthy mucosa at least 5 cm from the tumor tissue. From the controls, healthy stomach mucosa biopsies were collected. From all biopsies RNA and DNA were extracted. RNA was reverse transcribed into cDNA. V1-V2 region of bacterial 16S rRNA gene from all samples were amplified and sequenced on an Illumina MiSeq platform. Bray-Curtis algorithm was used to construct sample-similarity matrices abundances of taxonomic ranks in each sample type. For significant differences between groups permutational multivariate analysis of variance and Mann-Whitney test followed by false-discovery rate test were used.

RESULTS

Microbial analysis revealed that only a portion of phylotypes (18%-30%) overlapped between microbial profiles obtained from DNA and RNA samples. Detailed analysis revealed differences between GC and controls depending on the chosen modality, identifying 17 genera at the DNA level and 27 genera at the RNA level. Ten of those bacteria were found to be different from the control group at both levels. The key taxa showed congruent results in various tests used; however, differences in 7 bacteria taxa were found uniquely only at the DNA level, and 17 uniquely only at the RNA level. Furthermore, RNA sequencing was more sensitive for detecting differences in bacterial richness, as well as differences in the relative abundance of Reyranella and Sediminibacterium according to the type of GC. In each study group (control, tumor, and tumor adjacent) were found differences between DNA and RNA bacterial profiles.

CONCLUSION

Comprehensive microbial study provides evidence for the effect of choice of sequencing modality on the microbiota profile, as well as on the identified differences between case and control.

Out of the blue: the independent activity of sulfur-oxidizers and diatoms mediate the sudden color shift of a tropical river

BACKGROUND

Río Celeste ("Sky-Blue River") is a river located in the Tenorio National Park (Costa Rica) that has become an important hotspot for eco-tourism due to its striking sky-blue color. A previous study indicated that this color is not caused by dissolved chemical species, but by formation of light-scattering aluminosilicate particles at the mixing point of two colorless streams, the acidic Quebrada Agria and the neutral Río Buenavista.

RESULTS

We now present microbiological information on Río Celeste and its two tributaries, as well as a more detailed characterization of the particles that occur at the mixing point. Our results overturn the previous belief that the light scattering particles are formed by the aggregation of smaller particles coming from Río Buenavista, and rather point to chemical formation of hydroxyaluminosilicate colloids when Quebrada Agria is partially neutralized by Río Buenavista, which also contributes silica to the reaction. The process is mediated by the activities of different microorganisms in both streams. In Quebrada Agria, sulfur-oxidizing bacteria generate an acidic environment, which in turn cause dissolution and mobilization of aluminum and other metals. In Río Buenavista, the growth of diatoms transforms dissolved silicon into colloidal biogenic forms which may facilitate particle precipitation.

CONCLUSIONS

We show how the sky-blue color of Río Celeste arises from the tight interaction between chemical and biological processes, in what constitutes a textbook example of emergent behavior in environmental microbiology.

Enrichment of antibiotic resistance genes within bacteriophage populations in saliva samples from individuals undergoing oral antibiotic treatments

Spread of antibiotic resistance is a significant challenge for our modern health care system, and even more so in developing countries with higher prevalence of both infections and resistant bacteria. Faulty usage of antibiotics has been pinpointed as a driving factor in spread of resistant bacteria through selective pressure. However, horizontal gene transfer mediated through bacteriophages may also play an important role in this spread. In a cohort of Tanzanian patients suffering from bacterial infections, we demonstrate significant differences in the oral microbial diversity between infected and non-infected individuals, as well as before and after oral antibiotics treatment. Further, the resistome carried both by bacteria and bacteriophages vary significantly, with bla_CTX-M1 resistance genes being mobilized and enriched within phage populations. This may impact how we consider spread of resistance in a biological context, as well in terms of treatment regimes.

Effect of intra-partum azithromycin on the development of the infant nasopharyngeal microbiota: A post hoc analysis of a double-blind randomized trial

Background

Sepsis is a leading cause of neonatal death. Intrapartum azithromycin reduces neonatal nasopharyngeal carriage of potentially pathogenic bacteria, a prerequisite for sepsis. Early antibiotic exposure has been associated with microbiota perturbations with varying effects. This study aims to understand the effect of intrapartum azithromycin intervention on the developing nasopharyngeal microbiota of the child.

Methods

Using 16S rRNA gene sequencing, we analysed the microbiota of 343 nasopharyngeal samples collected from birth to 12 months from 109 healthy infants selected from a double-blind randomized placebo-controlled clinical trial conducted in the Gambia (PregnAnZI-1). In the trial, 829 women were given 2g oral azithromycin or placebo (1:1) during labour with the objective of reducing bacterial carriage in mother and child during the neonatal period. The post-hoc analysis presented here assessed the effect of the intervention on the child nasopharyngeal microbiota development.

Findings

55 children were from mothers given azithromycin and 54 from mothers given placebo. Comparing arms, we found an increase in alpha-diversity at day-6 (p = 0·018), and a significant effect on overall microbiota composition at days 6 and 28 (R² = 4.4%, q = 0·007 and R² = 2.3%, q = 0·018 respectively). At genus level, we found lower representation of Staphylococcus at day-6 (q = 0·0303) and higher representation of Moraxella at 12 months (q = 0·0443). Unsupervised clustering of samples by microbial community similarity showed different community dynamics between the intervention and placebo arms during the neonatal period.

Interpretation

These results indicate that intrapartum azithromycin caused short-term alterations in the nasopharyngeal microbiota with modest overall effect at 12 months of age. Further exploration of the effects of these variations on microbiome function will give more insight on the potential risks and benefits, for the child, associated with this intervention.

Funding

This work was jointly funded by the Medical Research Council (UK) (MC_EX_MR/J010391/1/MRC), Bill & Melinda Gates Foundation (OPP1196513), and MRCG@LSHTM Doctoral Training Program.

Capillimicrobium parvum gen. nov., sp. nov., a novel representative of Capillimicrobiaceae fam. nov. within the order Solirubrobacterales, isolated from a grassland soil

The order Solirubrobacterales is a deep-branching lineage within the phylum Actinomycetota . Most representatives have been isolated from terrestrial environments. A strain isolated from a grassland soil was found to be affiliated with this order and therefore characterized by a polyphasic approach. Cells of strain 0166_1T are Gram-positive, short rods, non-motile, non-spore-forming and divide by binary fission. A surface layer with protrusions covers the majority of the cells. Strain 0166_1T grows optimally around neutral to slightly alkaline pH (pH 7.1–7.9) and at temperatures between 24–36 °C in SSE/HD 1 : 10 medium. It grows optimally with 0–0.5% NaCl (w/v) but can withstand concentrations up to 5 %. The major fatty acids are C18 : 1 ω9c, C16 : 1  ω7c, C17 : 0 cyclo ω7c, C18 : 1  ω7c methyl and C19 : 0 cyclo ω9c. The major polar lipids are diphosphatidylglycerol, two unidentified phospholipids and one unidentified glycolipid. MK-7(H4) and MK-7(H2) are the predominant respiratory quinones. meso-2,6-Diaminopimelic acid is the diagnostic diamino acid in the cell-wall peptidoglycan. The G+C content for strain 0166_1T is 72.8 mol%. 16S rRNA gene sequence analysis indicated that this bacterium was related to Conexibacter arvalis KV-962T and Conexibacter stalactiti YC2-25T with 95.5 and 95.2 % sequence similarity, respectively. Based on the phenotypic, genomic and phylogenetic data, we propose the novel species Capillimicrobium parvum sp. nov. (type strain 0166_1T=DSM 104329T=LMG 29999T=CECT 9240T) of the novel genus Capillimicrobium gen. nov. within the novel family Capillimicrobiaceae fam. nov.

Characterization of Maladaptive Processes in Acute, Chronic and Remission Phases of Experimental Colitis in C57BL/6 Mice

Inflammatory bowel disease (IBD) is a chronic recurrent inflammatory disease with unknown etiology. Dextran sulfate sodium (DSS) induced colitis is a widely used mouse model in IBD research. DSS colitis involves activation of the submucosal immune system and can be used to study IBD-like disease characteristics in acute, chronic, remission and transition phases. Insight into colon inflammatory parameters is needed to understand potentially irreversible adaptations to the chronification of colitis, determining the baseline and impact of further inflammatory episodes. We performed analyses of non-invasive and invasive colitis parameters in acute, chronic and remission phases of the DSS colitis in C57BL/6 mice. Non-invasive colitis parameters poorly reflected inflammatory aspects of colitis in chronic remission phase. We found invasive inflammatory parameters, positively linked to repeated DSS-episodes, such as specific colon weight, inflamed colon area, spleen weight, absolute cell numbers of CD4+ and CD8+ T cells as well as B cells, blood IFN-γ level, colonic chemokines BLC and MDC as well as the prevalence of Turicibacter species in feces. Moreover, microbial Lactobacillus species decreased with chronification of disease. Our data point out indicative parameters of recurrent gut inflammation in context of DSS colitis.

Nasal Microbiota, Olfactory Health, Neurological Disorders and Aging—A Review

The nasal region is one of the distinct environments for the survival of various microbiota. The human microbial niche begins to inhabit the human body right from birth, and the microbiota survive as commensals or opportunistic pathogens throughout the life of humans in their bodies in various habitats. These microbial communities help to maintain a healthy microenvironment by preventing the attack of pathogens and being involved in immune regulation. Any dysbiosis of microbiota residing in the mucosal surfaces, such as the nasal passages, guts, and genital regions, causes immune modulation and severe infections. The coexistence of microorganisms in the mucosal layers of respiratory passage, resulting in infections due to their co-abundance and interactions, and the background molecular mechanisms responsible for such interactions, need to be considered for investigation. Additional clinical evaluations can explain the interactions among the nasal microbiota, nasal dysbiosis and neurodegenerative diseases (NDs). The respiratory airways usually act as a substratum place for the microbes and can act as the base for respiratory tract infections. The microbial metabolites and the microbes can cross the blood–brain barrier and may cause NDs, such as Parkinson’s disease (PD), Alzheimer’s disease (AD), and multiple sclerosis (MS). The scientific investigations on the potential role of the nasal microbiota in olfactory functions and the relationship between their dysfunction and neurological diseases are limited. Recently, the consequences of the severe acute respiratory syndrome coronavirus (SARS-CoV-2) in patients with neurological diseases are under exploration. The crosstalk between the gut and the nasal microbiota is highly influential, because their mucosal regions are the prominent microbial niche and are connected to the olfaction, immune regulation, and homeostasis of the central nervous system. Diet is one of the major factors, which strongly influences the mucosal membranes of the airways, gut, and lung. Unhealthy diet practices cause dysbiosis in gut microbiota and the mucosal barrier. The current review summarizes the interrelationship between the nasal microbiota dysbiosis, resulting olfactory dysfunctions, and the progression of NDs during aging and the involvement of coronavirus disease 2019 in provoking the NDs.

Gut microbial similarity in twins is driven by shared environment and aging

Background

Human gut microbiome composition is influenced by genetics, diet and environmental factors. We investigated the microbial composition in several gastrointestinal (GI) compartments to evaluate the impact of genetics, delivery mode, diet, household sharing and aging on microbial similarity in monozygotic and dizygotic twins.

Methods

Fecal, biopsy and saliva samples were obtained from total 108 twins. DNA and/or RNA was extracted and the region V1-V2 of the 16S rRNA gene was amplified and sequenced. Bray-Curtis similarity was used for further microbiome comparisons, Mann-Whitney test was applied to evaluate the significant differences between groups and Spearman test was applied to reveal potential correlations between data.

Findings

The global bacterial profiles were grouped into two clusters separating the upper and lower GI. The upper GI microbiome composition was strictly dependent on the Helicobacter pylori status. With a positivity rate of 55%, H. pylori completely colonized the stomach and separated infected twins from non-infected twins irrespective of zygosity status. Lower GI microbiome similarity between the twins was defined mainly by household-sharing and aging; whereas delivery mode and host genetics had no influence. There was a progredient decrease in the bacterial similarity with aging. Shared vs. non-shared phylotypes analysis showed that in both siblings the shared phylotypes progressively diminished with aging, while the non-shared phylotypes increased.

Interpretation

Our findings strongly highlight the aging and shared household as they key determinants in gut microbial similarity and drift in twins irrespective of their zygotic state.

Funding

This work was supported by the grant of the Research Council of Lithuania (Project no. APP-2/2016) and also partially supported by the funds of European Commission through the “European funds for regional development” (EFRE) as well as by the regional Ministry of Economy, Science and Digitalization as part of the “LiLife” Project as part of the “Autonomy in old Age” research group (Project ID: ZS/2018/11/95324).

Airway Microbiome and Serum Metabolomics Analysis Identify Differential Candidate Biomarkers in Allergic Rhinitis

Allergic rhinitis (AR) is a common heterogeneous chronic disease with a high prevalence and a complex pathogenesis influenced by numerous factors, involving a combination of genetic and environmental factors. To gain insight into the pathogenesis of AR and to identity diagnostic biomarkers, we combined systems biology approach to analyze microbiome and serum composition. We collected inferior turbinate swabs and serum samples to study the microbiome and serum metabolome of 28 patients with allergic rhinitis and 15 healthy individuals. We sequenced the V3 and V4 regions of the 16S rDNA gene from the upper respiratory samples. Metabolomics was used to examine serum samples. Finally, we combined differential microbiota and differential metabolites to find potential biomarkers. We found no significant differences in diversity between the disease and control groups, but changes in the structure of the microbiota. Compared to the HC group, the AR group showed a significantly higher abundance of 1 phylum (Actinobacteria) and 7 genera (Klebsiella, Prevotella and Staphylococcus, etc.) and a significantly lower abundance of 1 genus (Pelomonas). Serum metabolomics revealed 26 different metabolites (Prostaglandin D2, 20-Hydroxy-leukotriene B4 and Linoleic acid, etc.) and 16 disrupted metabolic pathways (Linoleic acid metabolism, Arachidonic acid metabolism and Tryptophan metabolism, etc.). The combined respiratory microbiome and serum metabolomics datasets showed a degree of correlation reflecting the influence of the microbiome on metabolic activity. Our results show that microbiome and metabolomics analyses provide important candidate biomarkers, and in particular, differential genera in the microbiome have also been validated by random forest prediction models. Differential microbes and differential metabolites have the potential to be used as biomarkers for the diagnosis of allergic rhinitis.

Transfer of FRozen Encapsulated multi-donor Stool filtrate for active ulcerative Colitis (FRESCO): study protocol for a prospective, multicenter, double-blind, randomized, controlled trial

Background

Ulcerative colitis (UC) is a chronic inflammatory bowel disease with significant morbidity and mortality. Although the precise cause remains unknown, disturbances in the intestinal microbial community have been linked to its pathogenesis. Randomized controlled trials in UC and relapsing Clostridioides difficile infection (CDI) have established fecal microbiota (FM) transfer (FMT) as an effective therapy. In this context, preliminary results indicated that the transfer of sterile fecal microbiota filtrates (<0.2 μm; FMF, FMFT) of donor stool also drives gastrointestinal microbiota changes and eliminates symptoms in CDI patients. However, along with the success of FMT, regulatory agencies issued safety alerts following reports of serious adverse events due to transmission of enteric pathogens through FMT. To reduce this risk, we established an extensive test protocol for our donors and quarantine regulations for the produced capsules, but alternative concepts are desirable.

Methods

Our project is a randomized, controlled, longitudinal, prospective, three-arm, multicenter, double-blind study to determine the safety and efficacy of repeated long-term, multi-donor FM or FMF transfers compared to placebo using oral, frozen capsules in 174 randomized patients with mild to moderate active UC. The primary outcome will be clinical remission at week 12.

Discussion

This proposal aims to examine (a) the efficacy of encapsulated transfer of FM and FMF as a therapy for mild to moderate UC, (b) the short- and long-term safety of FMT and FMFT in patients with UC, and (c) the microbial and immunologic changes that occur after FMT and FMFT to help understand how and why it affects inflammatory bowel disease.

Trial registration

ClinicalTrials.govNCT03843385. DRKS (Deutsches Register für Klinische Studien) DRKS00020471

Impact of healthy aging on active bacterial assemblages throughout the gastrointestinal tract

The adaption of gut microbiota (GM) throughout human life is a key factor in maintaining health. Interventions to restore a healthy GM composition may have the potential to improve health and disease outcomes in the elderly. We performed a comprehensive characterization of changes in the luminal and mucosa-associated microbiota composition in elderly compared with younger healthy individuals. Samples from saliva and feces, and biopsies from the upper and lower gastrointestinal tract (UGIT, LGIT), were collected from 59 asymptomatic individuals grouped by age: 40-55, 56-70, and 71-85 years). All underwent anthropometric, geriatric, and nutritional assessment. RNA was extracted and reverse-transcribed into complementary DNA; the V1-V2 regions of 16S ribosomal RNA genes were amplified and sequenced. Abundances of the taxa in all taxonomic ranks in each sample type were used to construct sample-similarity matrices by the Bray-Curtis algorithm. Significant differences between defined groups were assessed by analysis of similarity. The bacterial community showed strong interindividual variations and a clear distinction between samples from UGIT, LGIT, and feces. While in saliva some taxa were affected by aging, this number was considerably greater in UGIT and was subsequently higher in LGIT. Unexpectedly, aging scarcely influenced the bacterial community of feces over the age range of 40-85 years. The development of interventions to preserve and restore human health with increased age by establishing a healthy gut microbiome should not rely solely on data from fecal analysis, as the intestinal mucosa is affected by more significant changes, which differ from those observed in fecal analyses.

Human microbiota research in Africa: a systematic review reveals gaps and priorities for future research

BACKGROUND

The role of the human microbiome in health and disease is an emerging and important area of research; however, there is a concern that African populations are under-represented in human microbiome studies. We, therefore, conducted a systematic survey of African human microbiome studies to provide an overview and identify research gaps. Our secondary objectives were: (i) to determine the number of peer-reviewed publications; (ii) to identify the extent to which the researches focused on diseases identified by the World Health Organization [WHO] State of Health in the African Region Report as being the leading causes of morbidity and mortality in 2018; (iii) to describe the extent and pattern of collaborations between researchers in Africa and the rest of the world; and (iv) to identify leadership and funders of the studies.

METHODOLOGY

We systematically searched Medline via PubMed, Scopus, CINAHL, Academic Search Premier, Africa-Wide Information through EBSCOhost, and Web of Science from inception through to 1st April 2020. We included studies that characterized samples from African populations using next-generation sequencing approaches. Two reviewers independently conducted the literature search, title and abstract, and full-text screening, as well as data extraction.

RESULTS

We included 168 studies out of 5515 records retrieved. Most studies were published in PLoS One (13%; 22/168), and samples were collected from 33 of the 54 African countries. The country where most studies were conducted was South Africa (27/168), followed by Kenya (23/168) and Uganda (18/168). 26.8% (45/168) focused on diseases of significant public health concern in Africa. Collaboration between scientists from the United States of America and Africa was most common (96/168). The first and/or last authors of 79.8% of studies were not affiliated with institutions in Africa. Major funders were the United States of America National Institutes of Health (45.2%; 76/168), Bill and Melinda Gates Foundation (17.8%; 30/168), and the European Union (11.9%; 20/168).

CONCLUSIONS

There are significant gaps in microbiome research in Africa, especially those focusing on diseases of public health importance. There is a need for local leadership, capacity building, intra-continental collaboration, and national government investment in microbiome research within Africa. Video Abstract.

An Innovative Protocol for Metaproteomic Analyses of Microbial Pathogens in Cystic Fibrosis Sputum

Hallmarks of cystic fibrosis (CF) are increased viscosity of mucus and impaired mucociliary clearance within the airways due to mutations of the cystic fibrosis conductance regulator gene. This facilitates the colonization of the lung by microbial pathogens and the concomitant establishment of chronic infections leading to tissue damage, reduced lung function, and decreased life expectancy. Although the interplay between key CF pathogens plays a major role during disease progression, the pathophysiology of the microbial community in CF lungs remains poorly understood. Particular challenges in the analysis of the microbial population present in CF sputum is (I) the inhomogeneous, viscous, and slimy consistence of CF sputum, and (II) the high number of human proteins masking comparably low abundant microbial proteins. To address these challenges, we used 21 CF sputum samples to develop a reliable, reproducible and widely applicable protocol for sputum processing, microbial enrichment, cell disruption, protein extraction and subsequent metaproteomic analyses. As a proof of concept, we selected three sputum samples for detailed metaproteome analyses and complemented and validated metaproteome data by 16S sequencing, metabolomic as well as microscopic analyses. Applying our protocol, the number of bacterial proteins/protein groups increased from 199-425 to 392-868 in enriched samples compared to nonenriched controls. These early microbial metaproteome data suggest that the arginine deiminase pathway and multiple proteases and peptidases identified from various bacterial genera could so far be underappreciated in their contribution to the CF pathophysiology. By providing a standardized and effective protocol for sputum processing and microbial enrichment, our study represents an important basis for future studies investigating the physiology of microbial pathogens in CF in vivo – an important prerequisite for the development of novel antimicrobial therapies to combat chronic recurrent airway infection in CF.

Toll-like receptor 1 as a possible target in non-alcoholic fatty liver disease

Toll-like receptors (TLRs) in the liver compartment have repeatedly been attributed to the development of non-alcoholic fatty liver disease (NAFLD). Knowledge on TLR expression in blood cells and their relation to intestinal microbiota and NAFLD development is limited. Here, we determined TLR expression patterns in peripheral blood mononuclear cells (PBMCs) of NAFLD patients and controls, their relation to intestinal microbiota and the impact of TLRs found altered in NAFLD development. Markers of intestinal permeability in blood and TLR mRNA expression in PBMCs were determined in 37 NAFLD patients and 15 age-matched healthy controls. Fecal microbiota composition was evaluated in 21 NAFLD patients and 9 controls using 16S rRNA gene amplicon sequencing. Furthermore, TLR1^-/- and C57BL/6 mice (n = 5-6/group) were pair-fed a liquid control or a fat-, fructose- and cholesterol-rich diet. Intestinal microbiota composition and markers of intestinal permeability like zonulin and bacterial endotoxin differed significantly between groups with the latter markers being significantly higher in NAFLD patients. Expression of TLR1-8 and 10 mRNA was detectable in PBMCs; however, only TLR1 expression, being higher in NAFLD patients, were significantly positively correlated with the prevalence of Holdemanella genus while negative correlations were found with Gemmiger and Ruminococcus genera. TLR1^-/- mice were significantly protected from the development of diet-induced NAFLD when compared to wild-type mice. While intestinal microbiota composition and permeability differed significantly between NAFLD patients and healthy subjects, in PBMCs, only TLR1 expression differed between groups. Still, targeting these alterations might be a beneficial approach in the treatment of NAFLD in some patients.

The Upper Airway Microbiota, Environmental Exposures, Inflammation, and Disease

Along with playing vital roles in pathogen exclusion and immune system priming, the upper airways (UAs) and their microbiota are essential for myriad physiological functions such as conditioning and transferring inhaled air. Dysbiosis, a microbial imbalance, is linked with various diseases and significantly impedes the quality of one’s life. Daily inhaled exposures and/or underlying conditions contribute to adverse changes to the UA microbiota. Such variations in the microbial community exacerbate UA and pulmonary disorders via modulating inflammatory and immune pathways. Hence, exploring the UA microbiota’s role in maintaining homeostasis is imperative. The microbial composition and subsequent relationship with airborne exposures, inflammation, and disease are crucial for strategizing innovating UA diagnostics and therapeutics. The development of a healthy UA microbiota early in life contributes to normal respiratory development and function in the succeeding years. Although different UA cavities present a unique microbial profile, geriatrics have similar microbes across their UAs. This lost community segregation may contribute to inflammation and disease, as it stimulates disadvantageous microbial–microbial and microbial–host interactions. Varying inflammatory profiles are associated with specific microbial compositions, while the same is true for many disease conditions and environmental exposures. A shift in the microbial composition is also detected upon the administration of numerous therapeutics, highlighting other beneficial and adverse side effects. This review examines the role of the UA microbiota in achieving homeostasis, and the impact on the UAs of environmental airborne pollutants, inflammation, and disease.

Probiotic supplements alleviate gestational diabetes mellitus by restoring the diversity of gut microbiota: a study based on 16S rRNA sequencing

Probiotics effectively prevent and improve metabolic diseases such as diabetes by regulating the intestinal microenvironment and gut microbiota. However, the effects of probiotics in gestational diabetes mellitus are not clear. Here, we showed that probiotic supplements significantly improved fasting blood glucose in a gestational diabetes mellitus rat model. To further understand the mechanisms of probiotics in gestational diabetes mellitus, the gut microbiota were analyzed via 16S rRNA sequencing. We found that compared with the normal pregnant group, the gestational diabetes mellitus rats had decreased diversity of gut microbiota. Moreover, probiotic supplementation restored the diversity of the gut microbiota in gestational diabetes mellitus rats, and the gut microbiota structure tended to be similar to that of normal pregnant rats. In particular, compared with gestational diabetes mellitus rats, the abundance of Firmicutes and Actinobacteria was higher after probiotic supplementation. Furthermore, activating carbohydrate metabolism and membrane transport pathways may be involved in the potential mechanisms by which probiotic supplements alleviate gestational diabetes mellitus. Overall, our results suggested that probiotic supplementation might be a novel approach to restore the gut microbiota of gestational diabetes mellitus rats and provided an experimental evidence for the use of probiotic supplements to treat gestational diabetes mellitus.

Infant Gut Microbiota Associated with Fine Motor Skills

BACKGROUND

During early life, dynamic gut colonization and brain development co-occur with potential cross-talk mechanisms affecting behaviour.

METHODS

We used 16S rRNA gene sequencing to examine the associations between gut microbiota and neurodevelopmental outcomes assessed by the Bayley Scales of Infant Development III in 71 full-term healthy infants at 18 months of age. We hypothesized that children would differ in gut microbial diversity, enterotypes obtained by Dirichlet multinomial mixture analysis and specific taxa based on their behavioural characteristics.

RESULTS

In children dichotomized by behavioural trait performance in above- and below-median groups, weighted Unifrac b-diversity exhibited significant differences in fine motor (FM) activity. Dirichlet multinomial mixture modelling identified two enterotypes strongly associated with FM outcomes. When controlling for maternal pre-gestational BMI and breastfeeding for up to 3 months, the examination of signature taxa in FM groups showed that Turicibacter and Parabacteroides were highly abundant in the below-median FM group, while Collinsella, Coprococcus, Enterococcus, Fusobacterium, Holdemanella, Propionibacterium, Roseburia, Veillonella, an unassigned genus within Veillonellaceae and, interestingly, probiotic Bifidobacterium and Lactobacillus were more abundant in the above-median FM group.

CONCLUSIONS

Our results suggest an association between enterotypes and specific genera with FM activity and may represent an opportunity for probiotic interventions relevant to treatment for motor disorders.

Dulaglutide Alone and in Combination with Empagliflozin Attenuate Inflammatory Pathways and Microbiome Dysbiosis in a Non-Diabetic Mouse Model of NASH

Dysregulation of glucose homeostasis plays a major role in the pathogenesis of non-alcoholic steatohepatitis (NASH) as it activates proinflammatory and profibrotic processes. Beneficial effects of antiglycemic treatments such as GLP-1 agonist or SGLT-2 inhibitor on NASH in patients with diabetes have already been investigated. However, their effect on NASH in a non-diabetic setting remains unclear. With this aim, we investigated the effect of long-acting GLP1-agonist dulaglutide and SGLT-2 inhibitor empagliflozin and their combination in a non-diabetic mouse model of NASH. C57BL/6 mice received a high-fat-high-fructose (HFHC) diet with a surplus of cholesterol for 16 weeks. After 12 weeks of diet, mice were treated with either dulaglutide, empagliflozin or their combination. Dulaglutide alone and in combination with empagliflozin led to significant weight loss, improved glucose homeostasis and diminished anti-inflammatory and anti-fibrotic pathways. Combination of dulaglutide and empagliflozin further decreased MoMFLy6C^High and CD4⁺Foxp3⁺ T cells. No beneficial effects for treatment with empagliflozin alone could be shown. While no effect of dulaglutide or its combination with empaglifozin on hepatic steatosis was evident, these data demonstrate distinct anti-inflammatory effects of dulaglutide and their combination with empagliflozin in a non-diabetic background, which could have important implications for further treatment of NASH.

Usitatibacter rugosus gen. nov., sp. nov. and Usitatibacter palustris sp. nov., novel members of Usitatibacteraceae fam. nov. within the order Nitrosomonadales isolated from soil

Members of the metabolically diverse order Nitrosomonadales inhabit a wide range of environments. Two strains affiliated with this order were isolated from soils in Germany and characterized by a polyphasic approach. Cells of strains 0125_3^T and Swamp67^T are Gram-negative rods, non-motile, non-spore-forming, non-capsulated and divide by binary fission. They tested catalase-negative, but positive for cytochrome c-oxidase. Both strains form small white colonies on agar plates and grow aerobically and chemoorganotrophically on SSE/HD 1 : 10 medium, preferably utilizing organic acids and proteinaceous substrates. Strains 0125_3^T and Swamp67^T are mesophilic and grow optimally without NaCl addition at slightly alkaline conditions. Major fatty acids are C_16 : 1  ω7c, C_16 : 0 and C_14 : 0. The major polar lipids are diphosphatidylglycerol, phosphatidylethanolamine and phosphatidyglycerol. The predominant respiratory quinone is Q-8. The G+C content for 0125_3^T and Swamp67^T was 67 and 66.1 %, respectively. The 16S rRNA gene analysis indicated that the closest relatives (<91 % sequence similarity) of strain 0125_3^T were Nitrosospira multiformis ATCC 25196^T, Methyloversatilis universalis FAM5^T and Denitratisoma oestradiolicum AcBE2-1^T, while Nitrosospira multiformis ATCC 25196^T, Nitrosospira tenuis Nv1^T and Nitrosospira lacus APG3^T were closest to strain Swamp67^T. The two novel strains shared 97.4 % 16S rRNA gene sequence similarity with one another and show low average nucleotide identity of their genomes (83.8 %). Based on the phenotypic, chemotaxonomic, genomic and phylogenetic analysis, we propose the two novel species Usitatibacter rugosus sp. nov (type strain 0125_3^T=DSM 104443^T=LMG 29998^T=CECT 9241^T) and Usitatibacter palustris sp. nov. (type strain Swamp67^T=DSM 104440^T=LMG 29997^T=CECT 9242^T) of the novel genus Usitatibacter gen. nov., within the novel family Usitatibacteraceae fam. nov.

Effects of calcium level and source, formic acid, and phytase on phytate degradation and the microbiota in the digestive tract of broiler chickens

BACKGROUND

Diet acidification, dietary calcium (Ca) level, and phytase supplementation are known influences on the microbial community in the digestive tract and on phosphorus (P) utilization of broiler chickens. Effects of dietary factors and microbiota on P utilization may be linked because microorganisms produce enzymes that release P from phytate (InsP6), the main source of P in plant feedstuffs. This study aimed to detect linkages between microbiota and InsP6 degradation by acidifying diets (i.e., replacing Ca carbonate (CaCO3) by Ca formate or adding formic acid to CaCO3-containing diets), varying Ca levels, and supplementing phytase in a three-factorial design. We investigated i) the microbial community and pH in the digestive tract, ii) prececal (pc) P and Ca digestibility, and iii) InsP6 degradation.

RESULTS

All factors under investigation influenced digesta pH and the microbiota composition. Predicted functionality and relative abundance of microorganisms indicated that diets influenced the potential contribution of the microbiota on InsP degradation. Values of InsP6 degradation and relative abundance of the strains Lactobacillus johnsonii and Lactobacillus reuteri were correlated. Phytase supplementation increased pc InsP6 disappearance, with differences between Ca levels, and influenced concentrations of lower inositol phosphate isomers in the digestive tract. Formic acid supplementation increased pc InsP6 degradation to myo-inositol. Replacing CaCO3 by Ca-formate and the high level of these Ca sources reduced pc InsP6 disappearance, except when the combination of CaCO3 + formic acid was used. Supplementing phytase to CaCO3 + formic acid led to the highest InsP6 disappearance (52%) in the crop and increased myo-inositol concentration in the ileum digesta. Supplementing phytase leveled the effect of high Ca content on pc InsP6 disappearance.

CONCLUSIONS

The results point towards a contribution of changing microbial community on InsP6 degradation in the crop and up to the terminal ileum. This is indicated by relationships between InsP6 degradation and relative abundance of phosphatase-producing strains. Functional predictions supported influences of microbiota on InsP6 degradation. The extent of such effects remains to be clarified. InsP6 degradation may also be influenced by variation of pH caused by dietary concentration and solubility of the Ca in the feed.

Relative phytase efficacy values as affected by response traits, including ileal microbiota composition

The objective of this study was to compare the effects of graded inclusions of 2 phytase products and a mineral P source in broiler chickens using different response traits, including ileum microbiota composition. Eleven experimental diets were used. These were a low-P basal diet and diets supplemented with increasing levels of dicalcium phosphate (DCP), Natuphos E 5000 G (NE), or Natuphos 5000 G (N). The performance traits, prececal P digestibility, and tibia and foot ash results were subjected to regression analysis and slope ratios were used to compare the supplements based on the measured evaluation traits. In the microbiota analysis, total nucleic acids were extracted and the 16S rRNA gene was targeted for use in the amplicon sequencing process. Phylogenetic analysis was performed using Mothur, followed by a multivariate statistical analysis. The various response traits caused different estimates of relative efficacy. The mean results of all the response traits showed that a 1.75-fold increase in the activity of N was needed to achieve the same response as NE and the variability among the detected traits ranged from 1.59 (prececally digestible P intake) to 1.91 (amount of tibia ash). The mean slope ratio between DCP and NE was 311 and varied between 208 (ADG) and 349 (foot ash concentration). The mean slope ratio for phytase N with DCP was 552 and varied from 357 (ADG) to 640 (tibia ash concentration). The ileum microbiota composition was not different among the diets. A similar composition was driven in the abundance of Lactobacillus crispatus, Lactobacillus salivarius, and Lactobacillus gallinarum. The results suggest that different response traits cause markedly different estimates of relative phytase efficacy.

Microbiological findings in early and late implant loss: an observational clinical case-controlled study

Background

Implants are a predictable and well-established treatment method in dentistry. Nevertheless, looking at possible failures of dental implants, early and late loss have to be distinguished. The intent of the study was to report microbiological findings on the surface of implants with severe peri-implantitis, which had to be explanted.

Methods

53 specimens of implants from 48 patients without severe general illnesses have been examined. The groups investigated were implants that had to be removed in the period of osseointegration (early loss, 13 patients with 14 implants) or after the healing period (late loss, 14 patients with 17 implants). The implant losses were compared with two control groups (implants with no bone loss directly after completed osseointegration, two to four months after implant placement (17 patients with 17 implants) and implants with no bone loss and prosthetic restoration for more than three years (5 patients with 5 implants)). Data about the bacteria located in the peri-implant sulcus was collected using amplification and high throughput sequencing of the 16S rRNA gene.

Results

The biofilm composition differed substantially between individuals. Both in early and late implant loss, Fusobacterium nucleatum and Porphyromonas gingivalis were found to be abundant. Late lost implants showed higher bacterial diversity and in addition higher abundances of Treponema, Fretibacterium, Pseudoramibacter and Desulfobulbus, while microbial communities of early loss implants were very heterogeneous and showed no significantly more abundant bacterial taxa.

Conclusions

Specific peri-implant pathogens were found around implants that were lost after a primarily uneventful osseointegration. P. gingivalis and F. nucleatum frequently colonized the implant in early and late losses and could therefore be characteristic for implant loss in general. In general, early lost implants showed also lower microbial diversity than late losses. However, the microbial results were not indicative of the causes of early and late losses.

Design and evaluation of synthetic bacterial consortia for optimized phenanthrene degradation through the integration of genomics and shotgun proteomics

Two synthetic bacterial consortia (SC) composed of bacterial strains Sphingobium sp. (AM), Klebsiella aerogenes (B), Pseudomonas sp. (Bc-h and T), Burkholderia sp. (Bk) and Inquilinus limosus (Inq) isolated from a natural phenanthrene (PHN)-degrading consortium (CON) were developed and evaluated as an alternative approach to PHN biodegradation in bioremediation processes. A metabolic network showing the potential role of strains was reconstructed by in silico study of the six genomes and classification of dioxygenase enzymes using RHObase and AromaDeg databases. Network analysis suggested that AM and Bk were responsible for PHN initial attack, while Inq, B, T and Bc-h would degrade PHN metabolites. The predicted roles were further confirmed by physiological, RT-qPCR and metaproteomic assays. SC-1 with AM as the sole PHN degrader was the most efficient. The ecological roles inferred in this study can be applied to optimize the design of bacterial consortia and tackle the biodegradation of complex environmental pollutants.

Temporal Characteristics of the Oropharyngeal and Nasal Microbiota Structure in Crewmembers Stayed 180 Days in the Controlled Ecological Life Support System

Confined experiments are carried out to simulate the closed environment of space capsule on the ground. The Chinese Controlled Ecological Life Support System (CELSS) is designed including a closed-loop system supporting 4 healthy volunteers surviving for 180 days, and we aim to reveal the temporal characteristics of the oropharyngeal and nasal microbiota structure in crewmembers stayed 180 days in the CELSS, so as to accumulate the information about microbiota balance associated with respiratory health for estimating health risk in future spaceflight. We investigated the distribution of microorganisms and their dynamic characteristics in the nasal cavity and oropharynx of occupants with prolonged confinement. Based on the 16S rDNA v3–v4 regions using Illumina high-throughput sequencing technology, the oropharyngeal and nasal microbiota were monitored at eight time points during confinement. There were significant differences between oropharyngeal and nasal microbiota, and there were also individual differences among the same site of different volunteers. Analysis on the structure of the microbiota showed that, in the phylum taxon, the nasal bacteria mainly belonged to Actinobacteria, Firmicutes, Proteobacteria, Bacteroidetes, etc. In addition to the above phyla, in oropharyngeal bacteria Fusobacterial accounted for a relatively high proportion. In the genus taxon, the nasal and oropharyngeal bacteria were independent. Corynebacterium and Staphylococcus were dominant in nasal cavity, and Corynebacterium, Streptococcus, and Neisseria were dominant in oropharynx. With the extension of the confinement time, the abundance of Staphylococcus in the nasal cavity and Neisseria in the oropharynx increased, and the index Chao fluctuated greatly from 30 to 90 days after the volunteers entered the CELSS.

Conclusion: The structure and diversity of the nasal and oropharyngeal microbiota changed in the CELSS, and there was the phenomenon of migration between occupants, suggesting that the microbiota structure and health of the respiratory tract could be affected by living in a closed environment for a long time.

Removal of nickel(II) from wastewater using a zeolite-packed anaerobic bioreactor: Bacterial diversity and community structure shifts

In recent years, overexploited industrialization and urbanization activities have led to significant amounts of heavy metals released into the environment. Metal ion contamination of water, especially with toxic metals such as nickel(II) [Ni(II)], which is extensively applied in the electroplating industry, has been a serious problem. The aim of the present study was to evaluate the Ni(II) removal from real industrial wastewater using a 2 L, lab-scale, up-flow, anaerobic, zeolite-packed bioreactor inoculated with a heterotrophic consortium as the bioadsorbent. High-throughput sequencing of 16S rRNA genes revealed significant shifts in their bacterial diversity and structural composition along the bioreactor treatment location, where the bacterial genus was dominated by Kosmotogae followed by Firmicutes as Ruminococcus and Clostridium. However, Fervidobacterium and the Geobacter genus were absent at the end of the bioreactor treatment, suggesting that they play a key role in the beginning of Ni(II) removal anaerobic treatment. The physico-chemical results revealed that the Ni(II) removal rate was 99% for 250-500 ppm metal tested, with an efficient alkalinity rate and high production of biogas, which confirmed that anaerobic digestion of microorganisms was successfully performed through the process. Finally, this anaerobic bioreactor configuration offers an accessible and ecofriendly high-rate metal removal strategy from mining and electroplating effluents.

Lethal Neonatal Respiratory Failure by Perinatal Transmission of Ureaplasma Parvum after Maternal PPROM

A primiparous pregnant woman was admitted due to preterm premature rupture of membranes (PPROM) at 27+0 week of gestational age (WGA). Conventional vaginal microbiological analysis had no pathological finding. Management decisions based on national guidelines included antenatal corticoids, tocolytics and antibiotics. Unstoppable efforts of preterm labor in 28+0 WGA and supposed amniotic infection syndrome necessitated emergency cesarean section. The preterm infant underwent NICU therapy, developed an early-onset neonatal sepsis and therapy-refractory pulmonary insufficiency with consecutive right heart failure, resulting in death on the 36^th day of life. Microbiota analyses by 16Sr DNA sequencing was performed from maternal vaginal swabs and from neonatal pharyngeal swabs. Maternal antibiotic treatment resulted in depletion of physiological vaginal colonization with Lactobacillus crispatus. Ureaplasma parvum became the dominant vaginal microorganism at delivery and was detected in high relative abundance in the neonatal specimen. Progressive radiological air-space changes and interstitial pathologies associated with Ureaplasma infection (bronchopulmonary dysplasia type III) were seen early at the 3^rd and distinctly from 14^th day of life. This clearly demonstrates the need of vaginal colonization diagnostics in PPROM patients and awareness of the consecutive risks in the preterm. Vaginal microbiome analysis may allow individualized and targeted maternal and fetal diagnostic, prophylactic and therapeutic strategies to identify, protect and treat the high-risk neonates after PPROM.

Microbial Community Structure Along a Horizontal Oxygen Gradient in a Costa Rican Volcanic Influenced Acid Rock Drainage System

We describe the geochemistry and microbial diversity of a pristine environment that resembles an acid rock drainage (ARD) but it is actually the result of hydrothermal and volcanic influences. We designate this environment, and other comparable sites, as volcanic influenced acid rock drainage (VARD) systems. The metal content and sulfuric acid in this ecosystem stem from the volcanic milieu and not from the product of pyrite oxidation. Based on the analysis of 16S rRNA gene amplicons, we report the microbial community structure in the pristine San Cayetano Costa Rican VARD environment (pH = 2.94-3.06, sulfate ~ 0.87-1.19 g L^-1, iron ~ 35-61 mg L^-1 (waters), and ~ 8-293 g kg^-1 (sediments)). San Cayetano was found to be dominated by microorganisms involved in the geochemical cycling of iron, sulfur, and nitrogen; however, the identity and abundance of the species changed with the oxygen content (0.40-6.06 mg L^-1) along the river course. The hypoxic source of San Cayetano is dominated by a putative anaerobic sulfate-reducing Deltaproteobacterium. Sulfur-oxidizing bacteria such as Acidithiobacillus or Sulfobacillus are found in smaller proportions with respect to typical ARD. In the oxic downstream, we identified aerobic iron-oxidizers (Leptospirillum, Acidithrix, Ferrovum) and heterotrophic bacteria (Burkholderiaceae bacterium, Trichococcus, Acidocella). Thermoplasmatales archaea closely related to environmental phylotypes found in other ARD niches were also observed throughout the entire ecosystem. Overall, our study shows the differences and similarities in the diversity and distribution of the microbial communities between an ARD and a VARD system at the source and along the oxygen gradient that establishes on the course of the river.

Dose-Dependent Effects of Dietary Xylooligosaccharides Supplementation on Microbiota, Fermentation and Metabolism in Healthy Adult Cats

In order to investigate the effect and appropriate dose of prebiotics, this study evaluated the effect of two levels of xylooligosaccharides (XOS) in cats. Twenty-four healthy adult cats were divided into three groups: no-XOS control diet with 1% cellulose; low XOS supplementation (LXOS) with 0.04% XOS and 0.96% cellulose; and high XOS supplementation (HXOS) with 0.40% XOS and 0.60% cellulose. Both XOS groups increased blood 3-hydroxybutyryl carnitine levels and decreased hexadecanedioyl carnitine levels. Both XOS treatments displayed an increased bacterial abundance of Blautia, Clostridium XI, and Collinsella and a decreased abundance of Megasphaera and Bifidobacterium. LXOS groups increased fecal pH and bacterial abundance of Streptococcus and Lactobacillus, decreased blood glutaryl carnitine concentration, and Catenibacterium abundance. HXOS group showed a more distinct microbiome profile and higher species richness, and an increased bacterial abundance of Subdoligranulum, Ruminococcaceae genus (unassigned genus), Erysipelotrichaceae genus, and Lachnospiraceae. Correlations between bacterial abundances and blood and fecal parameters were also observed. In conclusion, XOS could benefit feline gut health by altering microbiota; its effects dependant on the dose. The higher-dose XOS increased bacterial populations that possibly promoted intestinal fermentation, while the lower dose altered populations of carbohydrate-metabolic microbiota and possibly modulated host metabolism. Low-dose prebiotics may become a trend in future studies.

A Comparative Study of Associated Microbiota Between Pig Farm and Pig Slaughterhouse in Guangdong, China

The goal of this study was to compare the microbiota in different pig-present settings in China. Bioaerosol samples from pig farms and slaughterhouses and nasal samples from pig farmers and slaughterhouse workers were collected in Guangdong, southern China. The bacterial genomic DNA was isolated and subjected to 16S sequencing. The data were analyzed using QIIME2 with the DADA2 pipeline. A total of 14,923,551 clean reads and 2785 operational taxonomic units (OTUs) were obtained, which were mostly grouped into 4 phyla (Proteobacteria, Bacteroidetes, Firmicutes, and Actinobacteria) and 220 families. The microbiota richness of nasal samples in pig-present workers was higher than that of bioaerosols collected in the vicinity of the pig enclosures. There were 31.7% (620/1954) shared OTUs between pig farm bioaerosols and pig farmers which was higher than that between pig slaughterhouses and slaughterhouse workers (23.4%, 364/1553) (p < 0.001). Acinetobacter and Pseudomonas were the most abundant in pig-present bioaerosols, and Staphylococcus, Pseudomonas, and Corynebacterium were dominant bacterial genus in pig farmers. The bacterial patterns are also specific to the location of sample collected. The results suggest that bioaerosol microbiota interact with human nasal microbes in the vicinity of the pig farm enclosures, providing the basis for further analysis of microbial transmission across hosts in pig-present settings.

Adhesion of Staphylococcus aureus to epithelial cells: an in vitro approach to study interactions within the nasal microbiota

Introduction. Staphylococcus aureus is a skin and mucous commensal bacterium of warm-blooded animals. In humans, the nose is the main ecological niche of S. aureus, and nasal carriage is a risk factor for developing an endogenous infection. S. aureus nasal colonization is a multifactorial process, involving inter-species interactions among the nasal microbiota.Aims. The objectives of this study were to characterize the microbiota of carriers and non-carriers of S. aureus and to demonstrate the importance of inter-species relationships in the adhesion of S. aureus, a key step in nasal colonization.Methodology. First, we characterized the nasal microbiota from 30 S. aureus carriers and non-carriers by a culturomic approach. We then evaluated the adhesion of S. aureus, first alone and then along with other bacteria of the nasal microbiota. To do that, we used an in vitro model to measure the interactions among bacteria in the presence of epithelial cells.Results. Analysis of the nasal microbiota of the carriers and non-carriers of S. aureus made it possible to observe that each microbiota has specific features in terms of composition. However, this composition differs significantly between carriers and non-carriers mainly through two bacterial groups: coagulase-negative staphylococci and corynebacteria. In a second part, adhesion of S. aureus to epithelial cells showed competition between S. aureus and these bacteria, suggesting a limitation of nasal colonization by S. aureus.Conclusion. These findings demonstrate the existence of a negative correlation between S. aureus and other species which inhibits adhesion and could limit nasal colonization.

16S Metagenomics Reveals Dysbiosis of Nasal Core Microbiota in Children With Chronic Nasal Inflammation: Role of Adenoid Hypertrophy and Allergic Rhinitis

Allergic rhinitis (AR) and adenoid hypertrophy (AH) are, in children, the main cause of partial or complete upper airway obstruction and reduction in airflow. However, limited data exist about the impact of the increased resistance to airflow, on the nasal microbial composition of children with AR end AH. Allergic rhinitis (AR) as well as adenoid hypertrophy (AH), represent extremely common pathologies in this population. Their known inflammatory obstruction is amplified when both pathologies coexist. In our study, the microbiota of anterior nares of 75 pediatric subjects with AR, AH or both conditions, was explored by 16S rRNA-based metagenomic approach. Our data show for the first time, that in children, the inflammatory state is associated to similar changes in the microbiota composition of AR and AH subjects respect to the healthy condition. Together with such alterations, we observed a reduced variability in the between-subject biodiversity on the other hand, these same alterations resulted amplified by the nasal obstruction that could constitute a secondary risk factor for dysbiosis. Significant differences in the relative abundance of specific microbial groups were found between diseased phenotypes and the controls. Most of these taxa belonged to a stable and quantitatively dominating component of the nasal microbiota and showed marked potentials in discriminating the controls from diseased subjects. A pauperization of the nasal microbial network was observed in diseased status in respect to the number of involved taxa and connectivity. Finally, while stable co-occurrence relationships were observed within both control- and diseases-associated microbial groups, only negative correlations were present between them, suggesting that microbial subgroups potentially act as maintainer of the eubiosis state in the nasal ecosystem. In the nasal ecosystem, inflammation-associated shifts seem to impact the more intimate component of the microbiota rather than representing the mere loss of microbial diversity. The discriminatory potential showed by differentially abundant taxa provide a starting point for future research with the potential to improve patient outcomes. Overall, our results underline the association of AH and AR with the impairment of the microbial interplay leading to unbalanced ecosystems.

Terricaulis silvestris gen. nov., sp. nov., a novel prosthecate, budding member of the family Caulobacteraceae isolated from forest soil

The family Caulobacteraceae comprises prosthecate bacteria with a dimorphic cell cycle and also non-prosthecate bacteria. Cells of all described species divide by binary fission. Strain 0127_4T was isolated from forest soil in Baden Württemberg (Germany) and determined to be the first representative of the family Caulobacteraceae which divided by budding. Cells of strain 0127_4T were Gram-negative, rod-shaped, prosthecate, motile by means of a polar flagellum, non-spore-forming and non-capsulated. The strain formed small white colonies and grew aerobically and chemo-organotrophically utilizing organic acids, amino acids and proteinaceous substrates. 16S rRNA gene sequence analysis indicated that this bacterium was related to Aquidulcibacter paucihalophilus TH1-2T and Asprobacter aquaticus DRW22-8T with 91.3 and 89.7% sequence similarity, respectively. Four unidentified glycolipids were detected as the major polar lipids and, unlike all described members of the family Caulobacteraceae , phosphatidylglycerol was absent. The major fatty acids were summed feature 8 (C18 : 1ω7c/C18 : 1ω6c), summed feature 9 (iso-C17 : 1ω9c/C16 : 0 10-methyl), C16 : 0 and summed feature 3 (C16 : 1 ω6c/C16 : 1 ω7c). The major respiratory quinone was Q-10. The G+C content of the genomic DNA was 63.5 %. Based on the present taxonomic characterization, strain 0127_4T represents a novel species of a new genus, Terricaulis silvestris gen. nov., sp. nov. The type strain of Terricaulis silvestris is 0127_4T (=DSM 104635T=CECT 9243T).

Oral Microbiota Display Profound Differential Metabolic Kinetics and Community Shifts upon Incubation with Sucrose, Trehalose, Kojibiose, and Xylitol

This study compares the metabolic properties of kojibiose, trehalose, sucrose, and xylitol upon incubation with representative oral bacteria as monocultures or synthetic communities or with human salivary bacteria in a defined medium. Compared to sucrose and trehalose, kojibiose resisted metabolism during a 48-h incubation with monocultures, except for Actinomyces viscosus Incubations with Lactobacillus-based communities, as well as salivary bacteria, displayed kojibiose metabolism, yet to a lesser extent than sucrose and trehalose. Concurring with our in vitro findings, screening for carbohydrate-active enzymes revealed that only Lactobacillus spp. and A. viscosus possess enzymes from glycohydrolase (GH) families GH65 and GH15, respectively, which are associated with kojibiose metabolism. Donor-dependent differences in salivary microbiome composition were noted, and differences in pH drop during incubation indicated different rates of sugar metabolism. However, functional analysis indicated that lactate, acetate, and formate evenly dominated the metabolic profile for all sugars except for xylitol. 16S rRNA gene sequencing analysis and α-diversity markers revealed that a significant shift of the microbiome community by sugars was more pronounced in sucrose and trehalose than in kojibiose and xylitol. In Streptococcus spp., a taxon linked to cariogenesis dominated in sucrose (mean ± standard deviation, 91.8 ± 6.4%) and trehalose (55.9 ± 38.6%), representing a high diversity loss. In contrast, Streptococcus (5.1 ± 3.7%) was less abundant in kojibiose, which instead was dominated by Veillonella (26.8 ± 19.6%), while for xylitol, Neisseria (29.4 ± 19.1%) was most abundant. Overall, kojibiose and xylitol incubations stimulated cariogenic species less yet closely maintained an abundance of key phyla and genera of the salivary microbiome, suggesting that kojibiose has low cariogenic properties.IMPORTANCE This study provides a detailed scientific insight on the metabolism of a rare disaccharide, kojibiose, whose mass production has recently been made possible. While the resistance of kojibiose was established with monocultures, delayed utilization of kojibiose was observed with communities containing lactobacilli and A. viscosus as well as with complex communities of bacteria from human saliva. Kojibiose is, therefore, less metabolizable than sucrose and trehalose. Moreover, although conventional sugars cause distinct shifts in salivary microbial communities, our study has revealed that kojibiose is able to closely maintain the salivary microbiome composition, suggesting its low cariogenic properties. This study furthermore underscores the importance and relevance of microbial culture and ex vivo mixed cultures to study cariogenicity and substrate utilization; this is in sharp contrast with tests that solely rely on monocultures such as Streptococcus mutans, which clearly fail to capture complex interactions between oral microbiota.

Stochasticity in microbiology: managing unpredictability to reach the Sustainable Development Goals

Pure (single) cultures of microorganisms and mixed microbial communities (microbiomes) have been important for centuries in providing renewable energy, clean water and food products to human society and will continue to play a crucial role to pursue the Sustainable Development Goals. To use microorganisms effectively, microbial engineered processes require adequate control. Microbial communities are shaped by manageable deterministic processes, but also by stochastic processes, which can promote unforeseeable variations and adaptations. Here, we highlight the impact of stochasticity in single culture and microbiome engineering. First, we discuss the concepts and mechanisms of stochasticity in relation to microbial ecology of single cultures and microbiomes. Second, we discuss the consequences of stochasticity in relation to process performance and human health, which are reflected in key disadvantages and important opportunities. Third, we propose a suitable decision tool to deal with stochasticity in which monitoring of stochasticity and setting the boundaries of stochasticity by regulators are central aspects. Stochasticity may give rise to some risks, such as the presence of pathogens in microbiomes. We argue here that by taking the necessary precautions and through clever monitoring and interpretation, these risks can be mitigated.

Development and validation of the Simulator of the Canine Intestinal Microbial Ecosystem (SCIME)1

Whereas a wide variety of in vitro models have been developed and validated to assess the effect of specific food ingredients on the human gut microbiome, such models have only been developed and applied to a limited extent for companion animals. Since the use of pre- and probiotics to improve gut health is an emerging research topic in the field of companion animals and as dogs are often used as laboratory animals in developing and testing of pharmaceuticals, the current study aimed to establish an adequate canine in vitro model. This consisted of a four-stage reactor composed of a stomach and small intestinal compartment followed by a proximal and distal colon. This semi-continuous gastrointestinal tract model allowed a long-term, region-dependent, and pH-controlled simulation of the colon-associated microbial community of dogs. Upon reaching a functional steady state, the simulated canine microbial community composition proved to be representative of the in vivo situation. Indeed, the predominant bacterial phyla present in the in vitro proximal and distal colon corresponded with the main bacterial phyla detected in the fecal material of the dogs, resulting in an average community composition along the simulated canine gastrointestinal tract of 50.5% Firmicutes, 34.5% Bacteroidetes, 7.4% Fusobacteria, 4.9% Actinobacteria, and 2.7% Proteobacteria. A parallel in vivo-in vitro comparison assessing the effects of fructooligosaccharides (FOS) on the canine microbial community composition showed a consistent stimulation of Lactobacillus concentrations in the in vivo fecal samples as well as in the in vitro canine gut model. Furthermore, the in vitro platform provided additional insights about the prebiotic effect of FOS supplementation of dogs, such as a reduced abundance of Megamonas spp. which are only present in very low abundance in in vivo fecal samples, indicating an interesting application potential of the developed canine in vitro model in research related to gastrointestinal health of dogs.

Microbiome-based body site of origin classification of forensically relevant blood traces

Human blood traces are amongst the most commonly encountered biological stains collected at crime scenes. Identifying the body site of origin of a forensic blood trace can provide crucial information in many cases, such as in sexual and violent assaults. However, means for reliably and accurately identifying from which body site a forensic blood trace originated are missing, but would be highly valuable in crime scene investigations. With this study, we introduce a taxonomy-independent deep neural network approach based on massively parallel microbiome sequencing, which delivers accurate body site of origin classification of forensically-relevant blood samples, such as menstrual, nasal, fingerprick, and venous blood. A total of 50 deep neural networks were trained using a large 16S rRNA gene sequencing dataset from 773 reference samples, including 220 female urogenital tract, 190 nasal cavity, 213 skin, and 150 venous blood samples. Validation was performed with de-novo generated 16S rRNA gene massively parallel sequencing (MPS) data from 94 blood test samples of four different body sites, and achieved high classification accuracy with AUC values at 0.992 for menstrual blood (N = 23), 0.978 for nasal blood (N = 16), 0.978 for fingerprick blood (N = 30), and 0.990 for venous blood (N = 25). The obtained highly accurate classification of menstrual blood was independent of the day of the menses, as established in additional 86 menstrual blood test samples. Accurate body site of origin classification was also revealed for 45 fresh and aged mock casework blood samples from all four body sites. Our novel microbiome approach works based on the assumption that a sample is from blood, as can be obtained in forensic practise from prior presumptive blood testing, and provides accurate information on the specific body source of blood, with high potentials for future forensic applications.

Hypericibacter terrae gen. nov., sp. nov. and Hypericibacter adhaerens sp. nov., two new members of the family Rhodospirillaceae isolated from the rhizosphere of Hypericum perforatum

Two strains of the family Rhodospirillaceae were isolated from the rhizosphere of the medicinal plant Hypericum perforatum. Cells of both strains were Gram-stain-negative, motile by means of a single polar flagellum, non-spore-forming, non-capsulated, short rods that divided by binary fission. Colonies were small and white. Strains R5913^T and R5959^T were oxidase-positive, mesophilic, neutrophilic and grew optimally without NaCl. Both grew under aerobic and microaerophilic conditions and on a limited range of substrates with best results on yeast extract. Major fatty acids were C_19 : 0 cyclo ω8c and C_16 : 0; in addition, C_18 : 1ω7c was also found as a predominant fatty acid in strain R5913^T. The major respiratory quinone was ubiquinone 10 (Q-10). The DNA G+C contents of strains R5913^T and R5959^T were 66.0 and 67.4 mol%, respectively. 16S rRNA gene sequence comparison revealed that the closest relatives (<92 % similarity) of the strains are Oceanibaculum pacificum MCCC 1A02656^T, Dongia mobilis CGMCC 1.7660^T, Dongia soli D78^T and Dongia rigui 04SU4-P^T. The two novel strains shared 98.6 % sequence similarity and represent different species on the basis of low average nucleotide identity of their genomes (83.8 %). Based on the combined phenotypic, genomic and phylogenetic investigations, the two strains represent two novel species of a new genus in the family Rhodospirillaceae, for which the name Hypericibacter gen. nov. is proposed, comprising the type species Hypericibacter terrae sp. nov. (type strain R5913^T=DSM 109816^T=CECT 9472^T) and Hypericibacter adhaerens sp. nov. (type strain R5959^T=DSM 109817^T=CECT 9620^T).

Longitudinal study of the bacterial and fungal microbiota in the human sinuses reveals seasonal and annual changes in diversity

There is a pressing need for longitudinal studies which examine the stability of the sinonasal microbiota. In this study, we investigated bacterial and fungal community composition of the sinuses of four healthy individuals every month for one year, then once every three months for an additional year to capture seasonal variation. Sequencing of bacterial 16S rRNA genes and fungal ITS2 revealed communities that were mainly dominated by members of Actinobacteria and Basidiomycota, respectively. We observed overall shifts in both bacterial and fungal community diversity that were attributable to a combination of individual, seasonal and annual changes. The results suggest that each of the subjects possessed a strong bacterial sinonasal signature, but that fungal communities were less subject specific. Differences in fungal and bacterial diversity between subjects, and which OTUs may be correlated with seasonal differences, were investigated. A small core community that persisted throughout the two year sampling period was identified: Corynebacterium, Propionibacterium and Staphylococcus, and one type of fungus, Malassezia restricta. It is likely that bacterial and fungal airway microbiomes are dynamic and experience natural shifts in diversity with time. The underlying reasons for these shifts appear to be a combination of changes in environmental climate and host factors.

Selecting the hologenome to breed for an improved feed efficiency in pigs-A novel selection index

Most traits in animal breeding, including feed efficiency traits in pigs, are affected by many genes with small effect and have a moderately high heritability between 0.1 and 0.5, which enables efficient selection. Since the microbiota composition in the gastrointestinal tract is also partly heritable and was shown to have a substantial effect on feed efficiency, the host genes affect the phenotype not only directly by altering metabolic pathways, but also indirectly by changing the microbiota composition. The effect m i of the microbiota composition on the breeding value g i of an animal i is the conditional expectation of its breeding value, given the vector φ i with microbiota frequencies, that is m i = E g i | φ i . The breeding value g i of an animal can therefore be decomposed into a heritable contribution m i that arises from an altered microbiota composition and a heritable contribution p i that arises from altered metabolic pathways within the animal, so g i = m i + p i . Instead of selecting for breeding value g ^ i , an index comprising the two components m ^ i and p ^ i with appropriate weights, that is I i = λ 1 m ^ i + λ 2 p ^ i , can be used. The present study shows how this breeding strategy can be applied in pig genomic selection breeding scheme for two feed efficiency traits and daily gain.

The microbiome of the upper respiratory tract in health and disease

The human upper respiratory tract (URT) offers a variety of niches for microbial colonization. Local microbial communities are shaped by the different characteristics of the specific location within the URT, but also by the interaction with both external and intrinsic factors, such as ageing, diseases, immune responses, olfactory function, and lifestyle habits such as smoking. We summarize here the current knowledge about the URT microbiome in health and disease, discuss methodological issues, and consider the potential of the nasal microbiome to be used for medical diagnostics and as a target for therapy.

Specific Wheat Fractions Influence Hepatic Fat Metabolism in Diet-Induced Obese Mice

Low whole grain consumption is a risk factor for the development of non-communicable diseases such as type 2 diabetes. Dietary fiber and phytochemicals are bioactive grain compounds, which could be involved in mediating these beneficial effects. These compounds are not equally distributed in the wheat grain, but are enriched in the bran and aleurone fractions. As little is known on physiological effects of different wheat fractions, the aim of this study was to investigate this aspect in an obesity model. For twelve weeks, C57BL/6J mice were fed high-fat diets (HFD), supplemented with one of four wheat fractions: whole grain flour, refined white flour, bran, or aleurone. The different diets did not affect body weight, however bran and aleurone decreased liver triglyceride content, and increased hepatic n-3 polyunsaturated fatty acid (PUFA) concentrations. Furthermore, lipidomics analysis revealed increased PUFA concentration in the lipid classes of phosphatidylcholine (PC), PC-ether, and phosphatidylinositol in the plasma of mice fed whole grain, bran, and aleurone supplemented diets, compared to refined white flour. Furthermore, bran, aleurone, and whole grain supplemented diets increased microbial α-diversity, but only bran and aleurone increased the cecal concentrations of short-chain fatty acids. The effects on hepatic lipid metabolism might thus at least partially be mediated by microbiota-dependent mechanisms.