Browsing by Subject "microbiota"

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  • Holster, Savanne; Hooiveld, Guido J.; Repsilber, Dirk; de Vos, Willem M.; Brummer, Robert J.; König, Julia (2019)
    Faecal microbiota transfer (FMT) consists of the introduction of new microbial communities into the intestine of a patient, with the aim of restoring a disturbed gut microbiota. Even though it is used as a potential treatment for various diseases, it is unknown how the host mucosa responds to FMT. This study aims to investigate the colonic mucosa gene expression response to allogenic (from a donor) or autologous (own) FMT in patients with irritable bowel syndrome (IBS). In a recently conducted randomised, double-blinded, controlled clinical study, 17 IBS patients were treated with FMT by colonoscopy. RNA was isolated from colonic biopsies collected by sigmoidoscopy at baseline, as well as two weeks and eight weeks after FMT. In patients treated with allogenic FMT, predominantly immune response-related gene sets were induced, with the strongest response two weeks after the FMT. In patients treated with autologous FMT, predominantly metabolism-related gene sets were affected. Furthermore, several microbiota genera showed correlations with immune-related gene sets, with different correlations found after allogenic compared to autologous FMT. This study shows that the microbe-host response is influenced by FMT on the mucosal gene expression level, and that there are clear differences in response to allogenic compared to autologous FMT.
  • Bui, Thi Phuong Nam; Troise, Antonio Dario; Fogliano, Vincenzo; de Vos, Willem M. (2019)
    Modifications of lysine contribute to the amount of dietary advanced glycation end-products reaching the colon. However, little is known about the ability of intestinal bacteria to metabolize dietary N-epsilon-carboxymethyllysine (CML). Successive transfers of fecal microbiota in growth media containing CML were used to identify and isolate species able to metabolize CML under anaerobic conditions. From our study, only donors exposed to processed foods degraded CML, and anaerobic bacteria enrichments from two of them used 77 and 100% of CML. Oscillibacter and Cloacibacillus evryensis increased in the two donors after the second transfer, highlighting that the bacteria from these taxa could be candidates for anaerobic CML degradation. A tentative identification of CML metabolites produced by a pure culture of Cloacibacillus evryensis was performed by mass spectrometry: carboxymethylated biogenic amines and carboxylic acids were identified as CML degradation products. The study confirmed the ability of intestinal bacteria to metabolize CML under anoxic conditions.
  • Koponen, Kari (Helsingin yliopisto, 2020)
    BACKGROUND: Diet has a major influence on the human gut microbiome, which has been linked to health and disease. However, epidemiological studies on the association of a healthy diet with the gut microbiome utilizing a whole-diet approach are still scant. OBJECTIVES: To assess associations between healthy food choices and human gut microbiome composition, and to determine the strength of association with the functional potential of the microbiome. DESIGN: The study sample consisted of 4,930 participants in the FINRISK 2002 study. Food intake was assessed using a food propensity questionnaire. Intake of food items recommended to be part of a healthy diet in the Nordic Nutrition Recommendations were transformed into a healthy food choices (HFC) score. Microbial diversity (alpha diversity) and compositional differences (beta diversity) and their associations with the HFC score and its components were assessed using linear regression and permutational multivariate analysis of variance (PERMANOVA). Associations between specific taxa and HFC were analyzed using multivariate associations with linear models (MaAsLin). Functional associations were derived from KEGG orthologies (KO) with linear regression models. RESULTS: Both microbial alpha (p = 1.90x10-4) and beta diversity (p ≤ 0.001) associated with HFC score. For alpha diversity, the strongest associations were observed for fiber-rich breads, poultry, fruits, and low-fat cheeses. For beta diversity, most prominent associations were observed for vegetables followed by berries and fruits. Genera with fiber-degrading and short-chain fatty acids (SCFA) producing capacity were positively associated with the HFC score. HFC associated positively with KO-based functions such as vitamin biosynthesis and SCFA metabolism, and inversely with fatty acid biosynthesis and the sulfur relay system. CONCLUSIONS: These results from a large and representative population-based survey confirm and extend findings of other smaller-scale studies that plant and fiber-rich dietary choices are associated with a more diverse and compositionally distinct microbiome, and with a greater potential to produce SCFAs.
  • Koponen, Kari K.; Salosensaari, Aaro; Ruuskanen, Matti O.; Havulinna, Aki S.; Männistö, Satu; Jousilahti, Pekka; Palmu, Joonatan; Salido, Rodolfo; Sanders, Karenina; Brennan, Caitriona; Humphrey, Gregory C.; Sanders, Jon G.; Meric, Guillaume; Cheng, Susan; Inouye, Michael; Jain, Mohit; Niiranen, Teemu J.; Valsta, Liisa M.; Knight, Rob; Salomaa, Veikko V. (2021)
    Background: Diet has a major influence on the human gut microbiota, which has been linked to health and disease. However, epidemiological studies on associations of a healthy diet with the microbiota utilizing a whole-diet approach are still scant. Objectives: To assess associations between healthy food choices and human gut microbiota composition, and to determine the strength of association with functional potential. Methods: This population-based study sample consisted of 4930 participants (ages 25-74; 53% women) in the FINRISK 2002 study. Intakes of recommended foods were assessed using a food propensity questionnaire, and responses were transformed into healthy food choices (HFC) scores. Microbial diversity (alpha diversity) and compositional differences (beta diversity) and their associations with the HFC score and its components were assessed using linear regression. Multiple permutational multivariate ANOVAs were run from whole-metagenome shallow shotgun-sequenced samples. Associations between specific taxa and HFC were analyzed using linear regression. Functional associations were derived from Kyoto Encyclopedia of Genes and Genomes orthologies with linear regression models. Results: Both microbial alpha diversity (beta/SD, 0.044; SE, 6.18 x 10(-5); P = 2.21 x 10(-3)) and beta diversity (R-2, 0.12; P Conclusions: Our results from a large, population-based survey confirm and extend findings of other, smaller-scale studies that plant and fiber-rich dietary choices are associated with a more diverse and compositionally distinct microbiota, and with a greater potential to produce SCFAs.
  • Giaretta, Paula R.; Suchodolski, Jan S.; Jergens, Albert E.; Steiner, Jorg M.; Lidbury, Jonathan A.; Cook, Audrey K.; Hanifeh, Mohsen; Spillmann, Thomas; Kilpinen, Susanne; Syrja, Pernilla; Rech, Raquel R. (2020)
    The intestinal microbiota is believed to play a role in the pathogenesis of inflammatory bowel disease in humans and chronic inflammatory enteropathy (CIE) in dogs. While most previous studies have described the gut microbiota using sequencing methods, it is fundamental to assess the spatial distribution of the bacteria for a better understanding of their relationship with the host. The microbiota in the colonic mucosa of 22 dogs with CIE and 11 control dogs was investigated using fluorescence in situ hybridization (FISH) with a universal eubacterial probe (EUB338) and specific probes for select bacterial groups. The number of total bacteria labeled with EUB338 probe was lower within the colonic crypts of dogs with CIE compared to controls. Helicobacter spp. and Akkermansia spp. were decreased on the colonic surface and in the crypts of dogs with CIE. Dogs with CIE had increased number of Escherichia coli/Shigella spp. on the colonic surface and within the crypts compared to control dogs. In conclusion, the bacterial microbiota in the colonic mucosa differed between dogs with and without CIE, with depletion of the crypt bacteria in dogs with CIE. The crypt bacterial species that was intimately associated with the host mucosa in control dogs was composed mainly of Helicobacter spp.
  • Biesiekierski, Jessica R.; Jalanka, Jonna; Staudacher, Heidi M. (2019)
    Dietary intervention is a challenge in clinical practice because of inter-individual variability in clinical response. Gut microbiota is mechanistically relevant for a number of disease states and consequently has been incorporated as a key variable in personalised nutrition models within the research context. This paper aims to review the evidence related to the predictive capacity of baseline microbiota for clinical response to dietary intervention in two specific health conditions, namely, obesity and irritable bowel syndrome (IBS). Clinical trials and larger predictive modelling studies were identified and critically evaluated. The findings reveal inconsistent evidence to support baseline microbiota as an accurate predictor of weight loss or glycaemic response in obesity, or as a predictor of symptom improvement in irritable bowel syndrome, in dietary intervention trials. Despite advancement in quantification methodologies, research in this area remains challenging and larger scale studies are needed until personalised nutrition is realistically achievable and can be translated to clinical practice.
  • Jalanka, Jonna; Cheng, Jing; Hiippala, Kaisa; Ritari, Jarmo; Salojärvi, Jarkko; Ruuska, Tarja; Kalliomaki, Marko; Satokari, Reetta (2020)
    Inflammatory bowel diseases (IBD), ulcerative colitis (UC) and Crohn's disease (CD), are chronic debilitating disorders of unknown etiology. Over 200 genetic risk loci are associated with IBD, highlighting a key role for immunological and epithelial barrier functions. Environmental factors account for the growing incidence of IBD, and microbiota are considered as an important contributor. Microbiota dysbiosis can lead to a loss of tolerogenic immune effects and initiate or exacerbate inflammation. We aimed to study colonic mucosal microbiota and the expression of selected host genes in pediatric UC. We used high-throughput 16S rDNA sequencing to profile microbiota in colonic biopsies of pediatric UC patients (n= 26) and non-IBD controls (n= 27). The expression of 13 genes, including five for antimicrobial peptides, in parallel biopsies was assessed with qRT-PCR. The composition of microbiota between UC and non-IBD differed significantly (PCoA,p= 0.001). UC children had a decrease in Bacteroidetes and an increase in several family-level taxa including Peptostreptococcaceae and Enterobacteriaceae, which correlated negatively with the expression of antimicrobial peptides REG3G and DEFB1, respectively. Enterobacteriaceae correlated positively with the expression siderophore binding protein LCN2 and Betaproteobacteria negatively with DEFB4A expression. The results indicate that reciprocal interaction of epithelial microbiota and defense mechanisms play a role in UC.
  • Kampmann, C.; Dicksved, J.; Engstrand, L.; Rautelin, H. (2016)
    In mice, specific species composition of gut microbiota enhances susceptibility to Campylobacter jejuni but little is known about the specific composition of the human gut microbiota in providing protection from infections caused by enteropathogens. Healthy adult individuals, who travelled in groups from Sweden to destinations with an estimated high risk for acquisition of Campylobacter infection, were enrolled. Faecal samples, collected before travelling and after returning home, were cultured for bacterial enteropathogens, and analysed for Campylobacter by PCR and for the species composition of the microbiota by 16S amplicon massive parallel sequencing. The microbiota compositions were compared between persons who became infected during their travel and those who did not. A total of 63 participants completed the study; 14 became infected with Campylobacter, two with Salmonella and 47 remained negative for the enteropathogens tested. After exclusion of samples taken after antimicrobial treatment, 49 individuals were included in the final analyses. Intra-individual stability of the microbiota was demonstrated for samples taken before travelling. The original diversity of the faecal microbiota was significantly lower among individuals who later became infected compared with those who remained uninfected. The relative abundances of bacteria belonging to the family Lachnospiraceae, and more specifically its two genera Dorea and Coprococcus, were significantly higher among those who remained uninfected. The travel-related infection did not significantly modify the faecal microbiota composition. Species composition of human gut microbiota is important for colonization resistance to Campylobacter infection. Especially individuals with a lower diversity are more susceptible to Campylobacter infection. (C) 2015 The Authors. Published by Elsevier Ltd on behalf of European Society of Clinical Microbiology and Infectious Diseases.
  • Ruokolainen, Lasse; Parkkola, Anna; Karkman, Antti; Sinkko, Hanna; Peet, Aleksandr; Hämäläinen, Anu-Maaria; von Hertzen, Leena; Tillmann, Vallo; Koski, Katriina; Virtanen, Suvi M.; Niemelä, Onni; Haahtela, Tari; Knip, Mikael (2020)
    Background Allergic diseases are more common in Finland than in Estonia, which-according to the biodiversity hypothesis-could relate to differences in early microbial exposures. Methods We aimed at defining possible microbial perturbations preceding early atopic sensitization. Stool, nasal and skin samples of 6-month-old DIABIMMUNE study participants with HLA susceptibility to type 1 diabetes were collected. We compared microbiotas of sensitized (determined by specific IgE results at 18 months of age) and unsensitized Estonian and Finnish children. Results Sensitization was differentially targeted between populations, as egg-specific and birch pollen-specific IgE was more common in Finland. Microbial diversity and community composition also differed; the genusAcinetobacterwas more abundant in Estonian skin and nasal samples. Particularly, the strain-level profile ofAcinetobacter lwoffiiwas more diverse in Estonian samples. Early microbiota was not generally associated with later sensitization. Microbial composition tended to differ between children with or without IgE-related sensitization, but only in Finland. While land-use pattern (ie green areas vs. urban landscapes around the children's homes) was not associated with microbiota as a whole, it associated with the composition of the genusAcinetobacter. Breastfeeding affected gut microbial composition and seemed to protect from sensitization. Conclusions In accordance with the biodiversity hypothesis, our results support disparate early exposure to environmental microbes between Finnish and Estonian children and suggest a significant role of the genusAcinetobacterin the allergy gap between the two populations. The significance of the observed differences for later allergic sensitization remains open.
  • Viitasalo, Liisa; Iltanen, Sari; Huhtala, Heini; Saavalainen, Päivi; Kaukinen, Katri; Lindfors, Katri; Kurppa, Kalle (2020)
    Risk of celiac disease (CD) is increased in relatives of CD patients due to genetic and possible environmental factors. We recently reported increased seropositivity to anti-Saccharomyces cerevisiae (ASCA), Pseudomonas fluorescens-associated sequence (anti-I2) and Bacteroides caccae TonB-linked outer membrane protein (anti-OmpW) antibodies in CD. We hypothesized these markers also to be overrepresented in relatives. Seropositivity and levels of ASCA, anti-I2 and anti-OmpW were compared between 463 first-degree relatives, 58 untreated and 55 treated CD patients, and 80 controls. CD-associated human leukocyte antigen (HLA)-haplotypes and transglutaminase (tTGab) and endomysium (EmA) antibodies were determined. One or more of the microbial antibodies was present in 75% of relatives, 97% of untreated and 87% of treated CD patients and 44% of the controls. The relatives had higher median ASCA IgA (9.13 vs. 4.50 U/mL, p <0.001), ASCA IgG (8.91 vs. 5.75 U/mL, p <0.001) and anti-I2 (absorbance 0.74 vs. 0.32, p <0.001) levels than controls. There was a weak, positive correlation between tTGab and ASCA (r = 0.31, p <0.001). Seropositivity was not significantly associated with HLA. To conclude, seropositivity to microbial markers was more common and ASCA and anti-I2 levels higher in relatives of CD patients than controls. These findings were not associated with HLA, suggesting the role of other genetic and environmental factors.
  • Terhonen, Eeva; Blumenstein, Kathrin; Kovalchuk, Andriy; Asiegbu, Fred O. (2019)
    Terrestrial plants including forest trees are generally known to live in close association with microbial organisms. The inherent features of this close association can be commensalism, parasitism or mutualism. The term microbiota has been used to describe this ecological community of plant-associated pathogenic, mutualistic, endophytic and commensal microorganisms. Many of these microbiota inhabiting forest trees could have a potential impact on the health of, and disease progression in, forest biomes. Comparatively, studies on forest tree microbiomes and their roles in mutualism and disease lag far behind parallel work on crop and human microbiome projects. Very recently, our understanding of plant and tree microbiomes has been enriched due to novel technological advances using metabarcoding, metagenomics, metatranscriptomics and metaproteomics approaches. In addition, the availability of massive DNA databases (e.g., NCBI (USA), EMBL (Europe), DDBJ (Japan), UNITE (Estonia)) as well as powerful computational and bioinformatics tools has helped to facilitate data mining by researchers across diverse disciplines. Available data demonstrate that plant phyllosphere bacterial communities are dominated by members of only a few phyla (Proteobacteria, Actinobacteria, Bacteroidetes). In bulk forest soil, the dominant fungal group is Basidiomycota, whereas Ascomycota is the most prevalent group within plant tissues. The current challenge, however, is how to harness and link the acquired knowledge on microbiomes for translational forest management. Among tree-associated microorganisms, endophytic fungal biota are attracting a lot of attention for their beneficial health- and growth-promoting effects, and were preferentially discussed in this review.
  • Raju, Sajan C.; Lagström, Sonja; Ellonen, Pekka; de Vos, Willem M.; Eriksson, Johan G.; Weiderpass, Elisabete; Rounge, Trine B. (2019)
    Objective: The human intestinal microbiota likely play an important role in the development of overweight and obesity. However, the associations between saliva microbiota and body mass index (BMI) have been sparsely studied. The aim of this study was to identify the associations between saliva microbiota and body size in Finnish children. Methods: The saliva microbiota of 900 Finnish children, aged 11-14 years with measured height and weight, was characterized using 16S rRNA (V3-V4) sequencing. Results: The core saliva microbiota consisted of 14 genera that were present in more than 95% of the Finnish children. The saliva microbiota profiles were gender-specific with higher alpha-diversity in boys than girls and significant differences between the genders in community composition and abundances. Alpha-diversity differed between normal weight and overweight girls and between normal weight and obese boys. The composition was dissimilar between normal weight and obese girls, but not in boys. The relative abundance profiles differed according to body size. Decrease in commensal saliva bacteria were observed in all the body sizes when compared to normal weight children. Notably, the relative abundance of bacteria related to, Veillonella, Prevotella, Selenomonas, and Streptococcus was reduced in obese children. Conclusion: Saliva microbiota diversity and composition were significantly associated with body size and gender in Finnish children. Body size-specific saliva microbiota profiles open new avenues for studying the potential roles of microbiota in weight development and management.
  • Afrizal (Helsingin yliopisto, 2017)
    Bacteria are dominant members of the human gut microbiota, defined as the complex communities of microorganisms in the intestine which play an important role in regulating the health of their host, including the development of colorectal cancer (CRC). CRC is the fourth leading cancer-related mortality worldwide. Animal models are very useful in CRC research, as they allow studying molecular mechanism underlying the disease. Due to closer similarity to human beings in terms of nutrition and gastrointestinal physiology, pig models are of great value in research when compared with murine models. However, our current knowledge of the pig gut microbiome is still limited and a large number of gut bacterial species are yet to be isolated and characterised. Here, we characterised bacteria isolated from the intestine of wildtype pigs and transgenic APC1311/+ siblings (APC pigs) that develop colonic adenomas. A total of 12 novel bacteria, including 1 member of a potentially novel family, were identified from 256 strains isolated using anaerobic culturing. In addition, five other bacteria with a standing name in the nomenclature but not yet included in the pig collection were added. A draft genome was generated for four of the novel bacteria and thereby the functional potential of strains and compared their similarity. In addition, the morphology, bile salt hydrolase (BSH), 7α-dehydroxylation, carbohydrate fermentation, prevalence and abundance of all strains were analysed. The draft genome analysis confirmed the novel species status of the four bacteria. Furthermore, it also revealed the presence of genes associated with BSH, antibiotic resistance, butyrate production and carbohydrate utilization. Only two of 12 tested bacteria were positive for BSH, while none of the two bacteria selected for fermentation experiments was positive for 7α-dehydroxylation. One isolate of the species Paraclostridium benzoelyticum was found to exhibit significantly higher tolerance to NaCl than the same species described in the literature. In terms of prevalence, almost all of the bacteria (16 of 17) seem to be rare in pig, even though they appeared to be more enriched in the pig intestine when compared with other host species. Interestingly, the majority of positive samples for the bacterium representing the potentially novel family originated from the intestine of elderly human individuals. Overall, we could show that a substantial number of novel bacteria can still be isolated by classical anaerobic culture techniques using multiple rich or selective media. Even though we were able to identify most of the isolated bacteria and performed several assays to describe their properties, additional phylogenetic and taxonomic tests and development of optimal media/conditions for the novel bacteria are required in order to gain a deeper understanding of the role of these bacteria in the intestinal microbial ecosystem.
  • Suh, Sang Heon; Choe, Kibaek; Hong, Seon Pyo; Jeong, Seung-hwan; Mäkinen, Taija; Kim, Kwang Soon; Alitalo, Kari; Surh, Charles D.; Koh, Gou Young; Song, Joo-Hye (2019)
    A lacteal is a blunt-ended, long, tube-like lymphatic vessel located in the center of each intestinal villus that provides a unique route for drainage of absorbed lipids from the small intestine. However, key regulators for maintaining lacteal integrity are poorly understood. Here, we explore whether and how the gut microbiota regulates lacteal integrity. Germ depletion by antibiotic treatment triggers lacteal regression during adulthood and delays lacteal maturation during the postnatal period. In accordance with compromised lipid absorption, the button-like junction between lymphatic endothelial cells, which is ultrastructurally open to permit free entry of dietary lipids into lacteals, is significantly reduced in lacteals of germ-depleted mice. Lacteal defects are also found in germ-free mice, but conventionalization of germ-free mice leads to normalization of lacteals. Mechanistically, VEGF-C secreted from villus macrophages upon MyD88-dependent recognition of microbes and their products is a main factor in lacteal integrity. Collectively, we conclude that the gut microbiota is a crucial regulator for lacteal integrity by endowing its unique microenvironment and regulating villus macrophages in small intestine.
  • Freitag, Tobias L.; Hartikainen, Anna; Jouhten, Hanne; Sahl, Cecilia; Meri, Seppo; Anttila, Veli-Jukka; Mattila, Eero; Arkkila, Perttu; Jalanka, Jonna; Satokari, Reetta (2019)
    Fecal microbiota transplantation (FMT) is an effective therapy for recurrent Clostridioides difficile infection (rCDI) and is also considered a potential treatment for a wide range of intestinal and systemic diseases. FMT corrects the microbial dysbiosis associated with rCDI, and the engraftment of donor microbiota is likely to play a key role in treatment efficacy. For disease indications other than rCDI, FMT treatment efficacy has been moderate. This may be partly due to stronger resilience of resident host microbiota in patients who do not suffer from rCDI. In rCDI, patients typically have undergone several antibiotic treatments prior to FMT, depleting the microbiota. In this study, we addressed the effect of broad-spectrum antibiotics (Ab) as a pre-treatment to FMT on the engraftment of donor microbiota in recipients. We conducted a pre-clinical study of FMT between two healthy mouse strains, Balb/c as donors and C57BL/6 as recipients, to perform FMT within the same species and to mimic interindividual FMT between human donors and patients. Microbiota composition was assessed with high-throughput 16S rDNA amplicon sequencing. The microbiota of Balb/c and C57BL/6 mice differed significantly, which allowed for the assessment of microbiota transplantation from the donor strain to the recipient. Our results showed that Ab-treatment depleted microbiota in C57BL/6 recipient mice prior to FMT. The diversity of microbiota did not recover spontaneously to baseline levels during 8 weeks after Ab-treatment, but was restored already at 2 weeks in mice receiving FMT. Interestingly, pre-treatment with antibiotics prior to FMT did not increase the overall similarity of the recipient's microbiota to that of the donor's, as compared with mice receiving FMT without Ab-treatment. Pre-treatment with Ab improved the establishment of only a few donor-derived taxa, such as Bifidobacterium, in the recipients, thus having a minor effect on the engraftment of donor microbiota in FMT. In conclusion, pre-treatment with broad-spectrum antibiotics did not improve the overall engraftment of donor microbiota, but did improve the engraftment of specific taxa. These results may inform future therapeutic studies of FMT.
  • Aivelo, Tuomas Juho Eero; Laakkonen, Juha Tapio; Jernvall, Jukka Tapani (2016)
    Longitudinal sampling for intestinal microbiota in wild animals is difficult, leading to a lack of information on bacterial dynamics occurring in nature. We studied how the composition of microbiota communities changed temporally in free-ranging small primates, rufous mouse lemurs (Microcebus rufus). We marked and recaptured mouse lemurs during their mating season in Ranomafana National Park in southeastern mountainous rainforests of Madagascar for 2 years and determined the fecal microbiota compositions of these mouse lemurs with MiSeq sequencing. We collected 160 fecal samples from 71 animals and had two or more samples from 39 individuals. We found small, but statistically significant, effects of site and age on microbiota richness and diversity and effects of sex, year, and site on microbiota composition, while the within-year temporal trends were less clear. Within-host microbiota showed pervasive variation in intestinal bacterial community composition, especially during the second study year. We hypothesize that the biological properties of mouse lemurs, including their small body size and fast metabolism, may contribute to the temporal intraindividual-level variation, something that should be testable with more-extensive sampling regimes.
  • Hemida, Manal B. M.; Salin, Siru; Vuori, Kristiina A.; Moore, Robin; Anturaniemi, Johanna; Rosendahl, Sarah; Barrouin-Melo, Stella Maria; Hielm-Bjorkman, Anna (2021)
    Background The increased prevalence of atopic dermatitis (AD) in dogs necessitates research in its disease etiology. Objectives To explore the association between puppyhood dietary exposures and prevalence of owner-reported allergy/atopy skin signs (AASS) after the age of 1 year. Animals Four thousand and twenty-two dogs were eligible, 1158 cases, and 2864 controls. Methods This cross-sectional hypothesis-driven observational study was extracted from the DogRisk food frequency questionnaire. Forty-six food items and the ratio of 4 major diet types were tested for their association with AASS incidence later in life. Potential puppyhood dietary risk factors for AASS incidence were specified using binary multivariable logistic regression. The model was adjusted for age and sex. Results Eating raw tripe (odds ratio, 95% confidence intervals OR, 95% CI = 0.36, 0.16-0.79; P = .01), raw organ meats (OR, 95% CI = 0.23, 0.08-0.67; P = .007), human meal leftovers, and fish oil supplements as well as eating more that 20% of the diet as raw and/or
  • Shetty, Sudarshan A.; Zuffa, Simone; Bui, Thi Phuong Nam; Aalvink, Steven; Smidt, Hauke; De Vos, Willem M. (2018)
    A bacterial strain designated L2-7(T), phylogenetically related to Eubacterium hallii DSM 3353(T), was previously isolated from infant faeces. The complete genome of strain L2-7(T) contains eight copies of the 16S rRNA gene with only 98.098.5 % similarity to the 16S rRNA gene of the previously described type strain E. hallii. The next closest validly described species is Anaerostipes hadrus DSM 3319(T) (90.7 % 16S rRNA gene similarity). A polyphasic taxonomic approach showed strain L2-7(T) to be a novel species, related to type strain E. hallii DSM 3353(T). The experimentally observed DNA-DNA hybridization value between strain L2-7(T) and E. hallii DSM 3353(T) was 26.25 %, close to that calculated from the genomes (34.3 %). The G+C content of the chromosomal DNA of strain L2-7(T) was 38.6 mol%. The major fatty acids were C-16(:0), C-16(:1) cis9 and a component with summed feature 10 (C-10(:1) c11/t9/t6c). Strain L2-7(T) had higher amounts of C-16:0 (30.6 %) compared to E. hallii DSM 3353(T) (19.5 %) and its membrane contained phosphatidylglycerol and phosphatidylethanolamine, which were not detected in E. hallii DSM 3353(T). Furthermore, 16S rRNA gene phylogenetic analysis advocates that E. hallii DSM 3353(T) is misclassified, and its reclassification as a member of the family Lachnospiraceae is necessary. Using a polyphasic approach, we propose that E. hallii (=DSM 3353(T)=ATCC 27751(T)) be reclassified as the type strain of a novel genus Anaerobutyricum sp. nov., comb. nov. and we propose that strain L2-7(T) should be classified as a novel species, Anaerobutyricum soehngenii sp. nov. The type strain is L2-7(T) (=DSM 17630(T) =KCIC 15707(T)).
  • Duplouy, Anne; Minard, Guillaume; Lähteenaro, Meri; Rytteri, Susu; Saastamoinen, Marjo (2018)
    All organisms are challenged by encounters with parasites, which strongly select for efficient escape strategies in the host. The threat is especially high for gregarious species entering immobile periods, such as diapause. Larvae of the Glanville fritillary butterfly, Melitaea cinxia, spend the winter in diapause in groups of conspecifics each sheltered in a silk nest. Despite intensive monitoring of the population, we have little understanding of the ecological factors influencing larval survival over the winter in the field. We tested whether qualitative and quantitative properties of the silk nest contribute to larval survival over diapause. We used comparative proteomics, metabarcoding analyses, microscopic imaging, and in vitro experiments to compare protein composition of the silk, community composition of the silk-associated microbiota, and silk density from both wild-collected and laboratory-reared families, which survived or died in the field. Although most traits assessed varied across families, only silk density was correlated with overwinter survival in the field. The silk nest spun by gregarious larvae before the winter acts as an efficient breathable physical shield that positively affects larval survival during diapause. Such benefit may explain how this costly trait is conserved across populations of this butterfly species and potentially across other silk-spinning insect species.
  • Rajilic-Stojanovic, Mirjana; de Vos, Willem M. (2014)