The Rhinobiome of Exacerbated Wheezers and Asthmatics: Insights From a German Pediatric Exacerbation Network

Although the nose, as a gateway for organism–environment interactions, may have a key role in asthmatic exacerbation, the rhinobiome of exacerbated children with asthma was widely neglected to date. The aim of this study is to understand the microbiome, the microbial immunology, and the proteome of exacerbated children and adolescents with wheeze and asthma. Considering that a certain proportion of wheezers may show a progression to asthma, the comparison of both groups provides important information regarding clinical and phenotype stratification. Thus, deep nasopharyngeal swab specimens, nasal epithelial spheroid (NAEsp) cultures, and blood samples of acute exacerbated wheezers (WH), asthmatics (AB), and healthy controls (HC) were used for culture (n = 146), 16 S-rRNA gene amplicon sequencing (n = 64), and proteomic and cytokine analyses. Interestingly, Proteobacteria were over-represented in WH, whereas Firmicutes and Bacteroidetes were associated with AB. In contrast, Actinobacteria commonly colonized HCs. Moreover, Staphylococcaceae, Enterobacteriaceae, Burkholderiaceae, Xanthobacteraceae, and Sphingomonadaceae were significantly more abundant in AB compared to WH and HC. The α-diversity analyses demonstrated an increase of bacterial abundance levels in atopic AB and a decrease in WH samples. Microbiome profiles of atopic WH differed significantly from atopic AB, whereby atopic samples of WH were more homogeneous than those of non-atopic subjects. The NAEsp bacterial exposure experiments provided a disrupted epithelial cell integrity, a cytokine release, and cohort-specific proteomic differences especially for Moraxella catarrhalis cultures. This comprehensive dataset contributes to a deeper insight into the poorly understood plasticity of the nasal microbiota, and, in particular, may enforce our understanding in the pathogenesis of asthma exacerbation in childhood.

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Gut Microbiome and Metabolome Profiles Associated with High-Fat Diet in Mice

Metabolites ◽

10.3390/metabo11080482 ◽

2021 ◽

Vol 11 (8) ◽

pp. 482

Author(s):

Jae-Kwon Jo ◽

Seung-Ho Seo ◽

Seong-Eun Park ◽

Hyun-Woo Kim ◽

Eun-Ju Kim ◽

...

Keyword(s):

Gut Microbiota ◽

Relative Abundance ◽

High Fat Diet ◽

Amplicon Sequencing ◽

Gas Chromatography Mass Spectrometry ◽

Control Group ◽

Rrna Gene ◽

High Fat ◽

Underlying Mechanisms ◽

Insight Into

Obesity can be caused by microbes producing metabolites; it is thus important to determine the correlation between gut microbes and metabolites. This study aimed to identify gut microbiota-metabolomic signatures that change with a high-fat diet and understand the underlying mechanisms. To investigate the profiles of the gut microbiota and metabolites that changed after a 60% fat diet for 8 weeks, 16S rRNA gene amplicon sequencing and gas chromatography-mass spectrometry (GC-MS)-based metabolomic analyses were performed. Mice belonging to the HFD group showed a significant decrease in the relative abundance of Bacteroidetes but an increase in the relative abundance of Firmicutes compared to the control group. The relative abundance of Firmicutes, such as Lactococcus, Blautia, Lachnoclostridium, Oscillibacter, Ruminiclostridium, Harryflintia, Lactobacillus, Oscillospira, and Erysipelatoclostridium, was significantly higher in the HFD group than in the control group. The increased relative abundance of Firmicutes in the HFD group was positively correlated with fecal ribose, hypoxanthine, fructose, glycolic acid, ornithine, serum inositol, tyrosine, and glycine. Metabolic pathways affected by a high fat diet on serum were involved in aminoacyl-tRNA biosynthesis, glycine, serine and threonine metabolism, cysteine and methionine metabolism, glyoxylate and dicarboxylate metabolism, and phenylalanine, tyrosine, and trypto-phan biosynthesis. This study provides insight into the dysbiosis of gut microbiota and metabolites altered by HFD and may help to understand the mechanisms underlying obesity mediated by gut microbiota.

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Variations in Facial Conformation Are Associated With Differences in Nasal Microbiota in Healthy Dogs

10.21203/rs.3.rs-69369/v1 ◽

2020 ◽

Author(s):

Emilie Vangrinsven ◽

Fastrès Aline ◽

Taminiau Bernard ◽

Frédéric Billen ◽

Daube Georges ◽

...

Keyword(s):

Living Environment ◽

Rrna Gene ◽

Intrinsic Factors ◽

Body Conformation ◽

Bacterial Microbiota ◽

Α Diversity ◽

Healthy Dogs ◽

Effect Of Age ◽

Nasal Microbiota ◽

Extrinsic And Intrinsic Factors

Abstract Background – Extrinsic and intrinsic factors have been shown to influence nasal microbiota (NM) in humans. Very few studies investigated the association between nasal microbiota and factors like facial/body conformation, age, and environment in dogs. Objectives are to investigate variations in NM in healthy dogs with different facial and body conformations and to assess the influence of age and living environment. A total of 46 dogs of different age, living environment and from 3 different breed groups were recruited: 22 meso-/dolichocephalic medium to large breed dogs, 12 brachycephalic dogs and 12 terrier breeds. The nasal bacterial microbiota was assessed through sequencing of 16S rRNA gene (V1-V3 regions) amplicons.Results – We showed major differences in the NM composition together with increased richness and α-diversity in brachycephalic dogs, compared to meso-/dolichocephalic dogs and dogs from terrier breeds. We failed to detect any effect of age or environment.Conclusion – Healthy brachycephalic breeds and their unique facial conformation is associated with a distinct NM profile. Description of the NM in healthy dogs serves as a foundation for future researches assessing the changes associated with disease and the modulation of NM communities as a potential treatment.

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Altered Nasal Microbiota Composition Associated with Development of Polyserositis by Mycoplasma hyorhinis

Pathogens ◽

10.3390/pathogens10050603 ◽

2021 ◽

Vol 10 (5) ◽

pp. 603

Author(s):

Miguel Blanco-Fuertes ◽

Florencia Correa-Fiz ◽

Lorenzo Fraile ◽

Marina Sibila ◽

Virginia Aragon

Keyword(s):

Pathological Finding ◽

Systemic Infection ◽

Amplicon Sequencing ◽

Rrna Gene ◽

Upper Respiratory Tract ◽

Mycoplasma Hyorhinis ◽

Predisposing Factor ◽

Glässer’S Disease ◽

Glasser's Disease ◽

Nasal Microbiota

Fibrinous polyserositis in swine farming is a common pathological finding in nursery animals. The differential diagnosis of this finding should include Glaesserella parasuis (aetiological agent of Glässer’s disease) and Mycoplasma hyorhinis, among others. These microorganisms are early colonizers of the upper respiratory tract of piglets. The composition of the nasal microbiota at weaning was shown to constitute a predisposing factor for the development of Glässer’s disease. Here, we unravel the role of the nasal microbiota in the subsequent systemic infection by M. hyorhinis, and the similarities and differences with Glässer’s disease. Nasal samples from farms with recurrent problems with polyserositis associated with M. hyorhinis (MH) or Glässer’s disease (GD) were included in this study, together with healthy control farms (HC). Nasal swabs were taken from piglets in MH farms at weaning, before the onset of the clinical outbreaks, and were submitted to 16S rRNA gene amplicon sequencing (V3–V4 region). These sequences were analyzed together with sequences from similar samples previously obtained in GD and HC farms. Animals from farms with disease (MH and GD) had a nasal microbiota with lower diversity than those from the HC farms. However, the composition of the nasal microbiota of the piglets from these disease farms was different, suggesting that divergent microbiota imbalances may predispose the animals to the two systemic infections. We also found variants of the pathogens that were associated with the farms with the corresponding disease, highlighting the importance of studying the microbiome at strain-level resolution.

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The Value of Vaginal Microbiome in Patients with Endometrial Hyperplasia

Journal of Healthcare Engineering ◽

10.1155/2021/4289931 ◽

2021 ◽

Vol 2021 ◽

pp. 1-7

Author(s):

Hu Zhang ◽

Qiao Feng ◽

Zhanpeng Zhu ◽

Haiyan Dai ◽

Hua Hu

Keyword(s):

Endometrial Hyperplasia ◽

Abnormal Uterine Bleeding ◽

Rrna Gene ◽

Vaginal Microbiome ◽

Bacterial Populations ◽

Α Diversity ◽

Significant Difference ◽

Proliferative Endometrium ◽

Microbial Dna ◽

Insight Into

Objective. To investigate the profiles of the vaginal microbiome in patients with endometrial hyperplasia and to explore the potential value of vaginal microbiome in the diagnosis of endometrial hyperplasia. Materials/Methods. 26 patients suffering from abnormal uterine bleeding (AUB) with thickened endometrium revealed by transvaginal ultrasonography were enrolled. Based on pathology, 12 patients with endometrial hyperplasia were classified as the Veh group and 14 patients with proliferative endometrium were classified as the Vne group. The vaginal samples were collected for the presence of microbial DNA by high-throughput next-generation sequencing of the 16S rRNA gene. The α-diversity and ß-diversity of vaginal microbiome were analyzed and compared between bacterial populations. The ROC curve was made to evaluate the feasibility of flora as a biomarker. Results. The diversity of vaginal microbiome in the Veh group was significantly lower than that in the Vne group ( P < 0.05 ). Lactobacillus was the most represented genus in the Veh group. The study’s t-test between the two groups showed that Lactobacillus has the only significant difference in the abundance of the first 15 genera ( P < 0.01 ). ROC analysis of the abundance of Lactobacillus showed that the area of AUC was 0.83, the sensitivity was 93.00%, and the specificity was 75.00%. Conclusion. The study offers insight into the nature of the vaginal microbiome and suggests that surveying the vaginal microbiota might be useful for detection of endometrial hyperplasia.

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Impact of Helicobacter pylori infection on fluid duodenal microbial community structure and microbial metabolic pathways

BMC Microbiology ◽

10.1186/s12866-022-02437-w ◽

2022 ◽

Vol 22 (1) ◽

Author(s):

Tadashi Maeda ◽

Hiroaki Zai ◽

Yuto Fukui ◽

Yoshifumi Kato ◽

Eri Kumade ◽

...

Keyword(s):

Helicobacter Pylori ◽

Metabolic Pathways ◽

Amplicon Sequencing ◽

Rrna Genes ◽

Rrna Gene ◽

Commensal Microbiota ◽

Operational Taxonomic Units ◽

H Pylori ◽

The Impact ◽

16 S Rrna

Abstract Background The bioactivities of commensal duodenal microbiota greatly influence the biofunction of hosts. We investigated the role of Helicobacter pylori infection in extra-gastroduodenal diseases by determining the impact of H. pylori infection on the duodenal microbiota. We sequenced 16 S rRNA genes in samples aspirated from the descending duodenum of 47 (male, 20; female, 27) individuals who were screened for gastric cancer. Samples were analysed using 16 S rRNA gene amplicon sequencing, and the LEFSe and Kyoto Encyclopaedia of Genes and Genomes methods were used to determine whether the duodenal microflora and microbial biofunctions were affected using H. pylori infection. Results Thirteen and 34 participants tested positive and negative for H. pylori, respectively. We identified 1,404 bacterial operational taxonomic units from 23 phyla and 253 genera. H. pylori infection changed the relative mean abundance of three phyla (Proteobacteria, Actinobacteria, and TM7) and ten genera (Neisseria, Rothia, TM7-3, Leptotrichia, Lachnospiraceae, Megasphaera, F16, Moryella, Filifactor, and Paludibacter). Microbiota features were significantly influenced in H. pylori-positive participants by 12 taxa mostly classified as Gammaproteobacteria. Microbial functional annotation revealed that H. pylori significantly affected 12 microbial metabolic pathways. Conclusions H. pylori disrupted normal bacterial communities in the duodenum and changed the biofunctions of commensal microbiota primarily by upregulating specific metabolic pathways. Such upregulation may be involved in the onset of diseases associated with H. pylori infection.

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Microbiome analyses of 12 psyllid species of the family Psyllidae identified various bacteria including Fukatsuia and Serratia symbiotica, known as secondary symbionts of aphids

BMC Microbiology ◽

10.1186/s12866-021-02429-2 ◽

2022 ◽

Vol 22 (1) ◽

Author(s):

Atsushi Nakabachi ◽

Hiromitsu Inoue ◽

Yuu Hirose

Keyword(s):

Plant Pathogens ◽

Amplicon Sequencing ◽

Rrna Gene ◽

Agricultural Pests ◽

Bacterial Populations ◽

Genus Level ◽

The Family ◽

Serratia Symbiotica ◽

First Time ◽

Insight Into

Abstract Background Psyllids (Hemiptera: Psylloidea) comprise a group of plant sap-sucking insects that includes important agricultural pests. They have close associations not only with plant pathogens, but also with various microbes, including obligate mutualists and facultative symbionts. Recent studies are revealing that interactions among such bacterial populations are important for psyllid biology and host plant pathology. In the present study, to obtain further insight into the ecological and evolutionary behaviors of bacteria in Psylloidea, we analyzed the microbiomes of 12 psyllid species belonging to the family Psyllidae (11 from Psyllinae and one from Macrocorsinae), using high-throughput amplicon sequencing of the 16S rRNA gene. Results The analysis showed that all 12 psyllids have the primary symbiont, Candidatus Carsonella ruddii (Gammaproteobacteria: Oceanospirillales), and at least one secondary symbiont. The majority of the secondary symbionts were gammaproteobacteria, especially those of the family Enterobacteriaceae (order: Enterobacteriales). Among them, symbionts belonging to “endosymbionts3”, which is a genus-level monophyletic group assigned by the SILVA rRNA database, were the most prevalent and were found in 9 of 11 Psyllinae species. Ca. Fukatsuia symbiotica and Serratia symbiotica, which were recognized only as secondary symbionts of aphids, were also identified. In addition to other Enterobacteriaceae bacteria, including Arsenophonus, Sodalis, and “endosymbionts2”, which is another genus-level clade, Pseudomonas (Pseudomonadales: Pseudomonadaceae) and Diplorickettsia (Diplorickettsiales: Diplorickettsiaceae) were identified. Regarding Alphaproteobacteria, the potential plant pathogen Ca. Liberibacter europaeus (Rhizobiales: Rhizobiaceae) was detected for the first time in Anomoneura mori (Psyllinae), a mulberry pest. Wolbachia (Rickettsiales: Anaplasmataceae) and Rickettsia (Rickettsiales: Rickettsiaceae), plausible host reproduction manipulators that are potential tools to control pest insects, were also detected. Conclusions The present study identified various bacterial symbionts including previously unexpected lineages in psyllids, suggesting considerable interspecific transfer of arthropod symbionts. The findings provide deeper insights into the evolution of interactions among insects, bacteria, and plants, which may be exploited to facilitate the control of pest psyllids in the future.

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Evidence for signatures of ancient microbial life in paleosols

Scientific Reports ◽

10.1038/s41598-020-73938-9 ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

Katharina Frindte ◽

Eva Lehndorff ◽

Stefan Vlaminck ◽

Katharina Werner ◽

Martin Kehl ◽

...

Keyword(s):

Bacterial Abundance ◽

Soil Formation ◽

Amplicon Sequencing ◽

Rrna Gene ◽

Soil Horizons ◽

Northern Iran ◽

Microbial Life ◽

Microbial Biomarkers ◽

Past Climate Change ◽

Loess Sediment

Abstract Loess-paleosol sequences are terrestrial archives of past climate change. They may host traces of ancient microbial life, but little information is available on the recovery of microbial biomarkers from such deposits. We hypothesized that microbial communities in soil horizons up to an age of 127 kyr carry information related to past environments. We extracted DNA from a loess-paleosol sequence near Toshan, Northern Iran, with 26 m thick deposits showing different degrees of soil development, performed quantitative PCR and 16S rRNA gene amplicon sequencing. Periods of soil formation archived within the loess sediment led to higher diversity and bacterial abundance in the paleosol horizons. Community composition fluctuated over the loess-paleosol sequence and was mainly correlated with age and depth, (ADONIS R2 < 0.14, P ≤ 0.002), while responses to paleosol soil traits were weaker. Phyla like Bacteriodetes, Proteobacteria or Acidobacteria were more prevalent in paleosol horizons characterized by intense soil formation, while weakly developed paleosols or loess horizons hosted a higher percentage and diversity of Actinobacteria. Taken together, our findings indicate that the microbial community in loess-paleosol sequences carries signatures of earlier environmental conditions that are preserved until today.

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Microbiomes of hadal fishes contain similar taxa, obligate symbionts, and known piezophiles across trench habitats

10.1101/2022.01.15.476391 ◽

2022 ◽

Author(s):

Jessica M Blanton ◽

Logan M Peoples ◽

Mackenzie E Gerringer ◽

Caroline M Iacuniello ◽

Natalya D Gallo ◽

...

Keyword(s):

Fatty Acids ◽

Hydrostatic Pressure ◽

Microbial Communities ◽

Deep Sea ◽

Deep Ocean ◽

Amplicon Sequencing ◽

Rrna Gene ◽

Mariana Trench ◽

Geographic Separation ◽

Insight Into

Hadal snailfishes are the deepest-living fishes in the ocean, inhabiting trenches from depths of ~6,000 to 8,000 m. While the microbial communities in trench environments have begun to be characterized, the microbes associated with hadal megafauna remain relatively unknown. Here, we describe the gut microbiomes of two hadal snailfishes, Pseudoliparis swirei (Mariana Trench) and Notoliparis kermadecensis (Kermadec Trench) using 16S rRNA gene amplicon sequencing. We contextualize these microbiomes with comparisons to the abyssal macrourid Coryphaenoides yaquinae and the continental shelf-dwelling snailfish Careproctus melanurus. The microbial communities of the hadal snailfishes were distinct from their shallower counterparts and were dominated by the same sequences related to the Mycoplasmataceae and Desulfovibrionaceae. These shared taxa indicate that symbiont lineages may have remained similar to the ancestral symbiont since their geographic separation or that they are dispersed between geographically distant trenches and subsequently colonize specific hosts. The abyssal and hadal fishes contained sequences related to known, cultured piezophiles, microbes that grow optimally under high hydrostatic pressure, including Psychromonas, Moritella, and Shewanella. These taxa are adept at colonizing nutrient-rich environments present in the deep ocean, such as on particles and in the guts of hosts, and we hypothesize they could make a dietary contribution to deep-sea fishes by degrading chitin and producing fatty acids. We characterize the gut microbiota within some of the deepest fishes to provide new insight into the diversity and distribution of host-associated microbial taxa and the potential of these animals, and the microbes they harbor, for understanding adaptation to deep-sea habitats.

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Continental-scale microbiome study reveals different environmental characteristics determining microbial richness and composition/quantity in hotel rooms

10.1101/849430 ◽

2019 ◽

Author(s):

Xi Fu ◽

Yanling Li ◽

Qianqian Yuan ◽

Gui-hong Cai ◽

Yiqun Deng ◽

...

Keyword(s):

Heavy Traffic ◽

Its Region ◽

Amplicon Sequencing ◽

Rrna Gene ◽

Microbial Composition ◽

Environmental Characteristics ◽

Continental Scale ◽

Β Diversity ◽

Α Diversity

AbstractCulture-independent microbiome surveys have been conducted in homes, hospitals, schools, kindergartens and vehicles for public transport, revealing diverse microbial distributions in built environments. However, microbiome surveys have not been conducted in hotel environments; thus, the composition and associated environmental factors are not clear. We presented the first continental-scale microbiome study of hotel rooms (n = 68) spanning large geographic regions. Bacterial and fungal communities were described by amplicon sequencing of the 16S rRNA gene and internal transcribed spacer (ITS) region and quantitative PCR. Similar numbers of bacterial (4,344) and fungal (4,555) operational taxonomic units were identified, but fungal taxa showed a local distribution compared with bacterial taxa. Aerobic, ubiquitous bacteria dominated the hotel microbiome with high compositional similarity to previous samples from building and human nasopharynx environments. The abundance of Aspergillus was negatively correlated with latitude and accounted for ∼80% of the total fungal load in seven low-latitude hotels. We calculated the association between hotel microbial dynamics and 16 indoor and outdoor environmental characteristics. Fungal β-diversity and quantity showed concordant variation and were associated with the same environmental characteristics, including latitude, quality of the interior, proximity to the sea and visible mold, while α-diversity decreased with heavy traffic (95% CI: −127.05 to −0.25) and wall-to-wall carpet (95% CI: −47.60 to −3.82). Bacterial β-diversity was associated with latitude, quality of the interior and floor type, while α-diversity decreased with recent decoration (95% CI −179.00 to −44.55) and mechanical ventilation (95% CI: −136.71 to −5.12).ImportanceThis is the first microbiome study to characterize microbial composition and associated environmental characteristics. In this study, we found concordant variation between microbial β-diversity and absolute quantity and discordant variation between β-diversity/quantity and α-diversity. Our study can be used to promote hotel hygiene standards and provide resource information for future microbiome and exposure studies associated with health effects in hotel rooms.

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Variations in facial conformation are associated with differences in nasal microbiota in healthy dogs

BMC Veterinary Research ◽

10.1186/s12917-021-03055-w ◽

2021 ◽

Vol 17 (1) ◽

Author(s):

Vangrinsven Emilie ◽

Fastrès Aline ◽

Taminiau Bernard ◽

Frédéric Billen ◽

Daube Georges ◽

...

Keyword(s):

Living Environment ◽

Rrna Gene ◽

Potential Treatment ◽

Intrinsic Factors ◽

Body Conformation ◽

Bacterial Microbiota ◽

Α Diversity ◽

Healthy Dogs ◽

Nasal Microbiota ◽

Extrinsic And Intrinsic Factors

Abstract Background Extrinsic and intrinsic factors have been shown to influence nasal microbiota (NM) in humans. Very few studies investigated the association between nasal microbiota and factors such as facial/body conformation, age, and environment in dogs. The objectives are to investigate variations in NM in healthy dogs with different facial and body conformations. A total of 46 dogs of different age, living environment and from 3 different breed groups were recruited: 22 meso−/dolichocephalic medium to large breed dogs, 12 brachycephalic dogs and 12 terrier breeds. The nasal bacterial microbiota was assessed through sequencing of 16S rRNA gene (V1-V3 regions) amplicons. Results We showed major differences in the NM composition together with increased richness and α-diversity in brachycephalic dogs, compared to meso−/dolichocephalic medium to large dogs and dogs from terrier breeds. Conclusion Healthy brachycephalic breeds and their unique facial conformation is associated with a distinct NM profile. Description of the NM in healthy dogs serves as a foundation for future researches assessing the changes associated with disease and the modulation of NM communities as a potential treatment.

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