An in silico investigation of anticancer peptide candidates in fermented food microbiomes

Objective: Cancer is a leading cause of death worldwide, requires development of new effective, specific, and safe strategies that do not carry the disadvantages of traditional cancer treatment approaches. Hence, this study aimed to identify anticancer peptide candidates in fermented food microbiomes through an in silico investigation. Materials and Methods: One hundred eight shotgun metagenomic sequencing samples from six studies on fermented food microbiomes were downloaded from the NCBI and ENA databases and included in the study. Bioinformatic analyses including quality control of raw data, de novo assembly, prediction of protein sequences, anticancer peptide predictions by an integrated use of four different prediction tools, toxicity predictions and database comparisons were performed. Results: One hundred forty-two novel anticancer peptide candidates were identified. Liquor, coffee, kefir fermentation samples contained the greatest numbers of anticancer peptide candidates while sugar, dairy, coconut kefir and brine-type fermentations were dominant sources according to the substrate type. Conclusion: This study indicates the potential of fermented food microbiomes as a useful source for candidate anticancer peptide detection. In vitro and in vivo validations of detected peptides may lead to development of new candidate molecules for cancer therapy in the future

Tip 2 diyabetik hastaların birinci derece yakınlarında total homosistein ve asimetrik dimetilargininin plazma düzeyleri

Amaç: Tip 2 diyabetik hastaların birinci derece yakınlarında, ailesinde diyabet öyküsü olmayan sağlıklı olgulara göre kardiyovasküler hastalıklar daha sık görülmektedir. Asimetrik dimetilarginin (ADMA) ve homosistein (Hcy) plazma düzeyleri kardiyovasküler hastalıklar ve endotel disfonksiyonuyla ilişkili göstergelerdir. Bu çalışmada, tip 2 diyabetik hastaların birinci derece yakınlarında ADMA ve Hcy plazma düzeyleri ile bu göstergelerle kardiyovasküler risk faktörleri arasındaki ilişkilerin incelenmesi amaçlandı. Hastalar ve Yöntemler: Dolaşımdaki ADMA ve Hcy düzeyleri 15 tip 2 diyabet hastasının birinci derece yakınında ve ailesinde diyabet öyküsü olmayan 15 kontrol olgusunda ölçüldü. Bulgular: Her iki grup arasında ADMA ve Hcy plazma düzeyleri açısından anlamlı farklılık saptanmadı (p>0.05). Asimetrik dimetilarginin plazma düzeyi tip 2 diyabetik olguların birinci derece yakınlarında, bel çevresi (p=0.02), açlık insülin düzeyi (p=0.03), insülin direnci (p=0.01), total kolesterol (p=0.04) ve HDL kolesterol (p=0.03) ile ilişkiliydi. Sonuç: Bu sonuçlara göre, kardiyovasküler risk faktörlerine sahip olan tip 2 diyabetik olguların birinci derece yakınlarında, ADMA plazma düzeylerinin doğrudan endotel disfonksiyonunun gelişimine katkıda bulunmadığını düşünmekteyiz.Objectives: Cardiovascular diseases are more common among first degree relatives of type 2 diabetic patients than healthy subjects without a family history of diabetes. Plasma asymmetric dimethylarginine (ADMA) and homocysteine (Hcy) levels are markers of endothelial dysfunction and cardiovascular disease. The objective of this study was to evaluate levels of ADMA, Hcy and their association with cardiovascular risk factors in first degree relatives of type 2 diabetic patients. Patients and Methods: The circulating ADMA and Hcy levels were measured in 15 first degree relatives of type 2 diabetic patients and 15 control subjects without a known family history of diabetes. Results: No statistically significant differences were found in plasma levels of ADMA and Hcy between the two groups (p>0.05). Plasma ADMA levels correlated significantly with waist circumference (p=0.02), fasting insulin levels (p=0.03), insulin resistance (p=0.01), total cholesterol (p=0.04) and HDL-cholesterol (p=0.03) levels in the first degree relatives of type 2 diabetic patients. Conclusion: These results suggest that plasma ADMA levels do not directly contribute to the development of endothelial dysfunction in first degree relatives of type 2 diabetic patients with cardiovascular risk factors

Obez hastalarda proinflamatuvar sitokinler ile fibrinolitik sistem arasındaki ilişki

Amaç: Obez kişilerde proinflamatuar sitokinlerden TNF-? ve IL-6, fibrinolitik sistem parametrelerinden t-PA ve PAI-1 ve insülin direnci arasındaki ilişki araştırıldı. Hastalar ve Yöntemler: Çalışmaya obez (VKİ ?30 kg/m2) olarak değerlendirilen 54 kişi (41 kadın, 13 erkek; ort. yaş 33.5) ve obezite sorunu olmayan (VKİ <25 kg/m2) 30 kişi (19 kadın, 11 erkek; ort. yaş 22.3) alındı. Fibrinojen düzeyleri koagülometrik olarak ve TNF-?, IL-6, t-PA, PAI-1 düzeyleri ELISA yöntemiyle ölçüldü. Bulgular: Kontrol grubuyla karşılaştırıldığında, obez kişilerde fibrinojen (p<0.01), PAI-1 (p<0.001), TNF-? (p<0.01) ve IL-6 düzeyleri (p<0.001) anlamlı derecede yüksek, t-PA düzeyi (p<0.001) ve t-PA/PAI-1 oranı (p<0.001) anlamlı derecede düşük bulundu. Obezlerde TNF-? ile t-PA (p=0.007) ve t-PA/PAI-1 oranı (p=0.016) arasında ters ilişki saptandı. İnsülin direnci olan ve olmayan obez kişilerde parametreler arasında fark yoktu. Sonuç: Obezitede adipoz dokudan salgılanan özellikle TNF-? gibi inflamatuar sitokinlerin artması fibrinolizde azalmaya yol açar. Obez kişilerde görülen bu değişiklikler, insülin direncinden bağımsız olarak ateroskleroza neden olabilir.Objectives: The aim of this study was to investigate the relationship between proinflammatory cytokines (TNF-&amp;#945; and IL-6), and fibrinolytic system parameters (t-PA, and PAI-1) and insulin resistance in obese individuals. Patients and Methods: The study included 54 obese subjects (BMI &amp;#8805;30 kg/m2; 41 females, 13 males; mean age 33.5 years) and 30 non-obese healthy individuals (BMI &lt;25 kg/m2; 19 females, 11 males; mean age 22.3 years). Fibrinogen levels were measured by the coagulometric method and the measurements of TNF-&amp;#945;, IL-6, t-PA and PAI-1 were carried out by the ELISA method. Results: Compared with non-obese subjects, obese individuals had significantly higher fibrinogen (p&lt;0.01), PAI-1 (p&lt;0.001), TNF-&amp;#945; (p&lt;0.01), and IL-6 (p&lt;0.001) levels, and significantly lower t-PA level (p&lt;0.001) and t-PA/PAI-1 ratio (p&lt;0.001). We also found an inverse relationship between TNF-&amp;#945; and t-PA levels (p=0.007) and t-PA/PAI-1 ratio (p=0.016) in obese individuals. The presence or absence of insulin resistance did not affect proinflammatory cytokines and fibrinolytic system parameters in obese individuals. Conclusion: Our findings indicate increased inflammatory cytokine levels especially in TNF-&amp;#945; level, and decreased fibrinolysis in obese individuals. These changes may contribute to atherosclerotic process independent from insulin resistance in obesity

Investigation of the Relationship Between Akkermansia Genomic Diversity in Gut Microbiota and Parkinson’s Disease Dementia

Parkinson hastalığında (PH), genellikle sağlıkla ilişkilendirilen bir bakteri cinsi olan Akkermansia’nın bağırsak mikrobiyotasında artış gösterdiği bilinse de bu artışın nedeni tam olarak anlaşılamamıştır. Bu çalışmada Türkiye’deki PH hastalarında, bağırsak mikrobiyotasındaki muhtemel Akkermansia değişimlerinin belirlenmesi amaçlanmıştır. Bu amaçla, ilk kez shotgun metagenomik ve Akkermansia cinsine özgül bir yeni nesil dizileme (NGS) tekniği kullanılarak PH’de bilişsel bozukluk evreleriyle ilişkili olabilecek belirli Akkermansia suşlarının varlığı ve bu suşlarda bulunan potansiyel genler incelenmiştir. Bu kapsamda Türkiye’de toplanmış dört bağırsak mikrobiyotası örneği -üç demanslı PH (PHD) ve bir bilişsel bozukluğu olmayan sağlıklı kontrol (SK)- shotgun metagenomik dizileme yoluyla analiz edilmiş ve örneklerdeki Akkermansia cinsine ait genomlar yeniden inşa edilmiştir. Bu genomlar, veri tabanlarındaki Akkermansia cinsine ait genomlarla bir araya getirilerek özel bir veri tabanı oluşturulmuş ve Akkermansia cinsine özgül NGS uyumlu primerler bu veri tabanı kullanılarak tasarlanmıştır. Hedef gen bölgesinin çoğaltılması ve cins özgül yeni nesil dizileme için kütüphane hazırlama basamaklarının optimize edilmesinden sonra, 64 PH hastası [32 PHD ve 32 hafif bilişsel bozukluk gösteren PH (PH-MCI)] ile 26 SK’ye ait bağırsak mikrobiyotası örnekleri cins özgül amplikon dizileme ile analiz edilmiştir. Analizler sonucunda, bağırsak mikrobiyotası örneklerinde Akkermansia muciniphila türüne ait oldukları belirlenen yedi suşun varlığı tespit edilmiş ve iki suşun demanslı (PHD) ve demansı olmayan (PH-MCI, HC) gruplar arasındaki dağılımının anlamlı farklılık gösterdiği (p< 0.05) belirlenmiştir. Tespit edilen suşlara ait genomların gen içerikleri, karşılaştırmalı genomik analizler yoluyla incelediğinde yalnızca dağılımı demanslı ve demansı olmayan gruplar arasında anlamlı farklılık gösteren iki suşta bulunan 12 genin varlığı tahmin edilmiştir. Bu genlerin annotasyonları yapıldığında ise daha önce rapor edilmemiş ve işlevi bilinmeyen genler oldukları görülmüştür. Bu çalışmada, ilk kez Türkiye’de toplanmış PH hastalarına ait bağırsak mikrobiyotası örneklerinin shotgun metagenomik analizleri gerçekleştirilmiş, özel olarak Akkermansia cinsinin analizi için cins-özgül bir amplikon dizileme yöntemi geliştirilmiş ve bu yöntem kullanılarak PH’de bilişsel bozukluk evreleriyle ile ilişkili olabilecek Akkermansia suşları ve genleri tespit edilmiştir. Elde edilen sonuçlar, tür ya da suş düzeyindeki farklılıkların araştırılmasının, bağırsak mikrobiyotasındaki PH ile ilişkili değişimlerin daha iyi anlaşılmasına yardımcı olabileceğine işaret etmektedir.Although it is known that the relative abundance of Akkermansia, a bacterial genus commonly associated with health, increases in the gut microbiota of Parkinson’s disease (PD) patients, the exact reason for this increase remains unclear. This study was aimed to identify potential changes in Akkermansia within the gut microbiota of PD patients in Türkiye. For this purpose, shotgun metagenomics and a novel Akkermansia genus-specific amplicon sequencing technique was used to investigate the presence of specific Akkermansia strains associated with cognitive impairment (CI) stages in PD and to examine potential genes within these strains. In this context, four gut microbiota samples from Türkiye -three PD with dementia (PDD) and one healthy control without CI (HC)- were analyzed by shotgun metagenomics and metagenome-assembled genomes assigned to Akkermansia genus were reconstructed. Then, a custom database was created by combining these genomes with the Akkermansia genomes in public databases and next generation sequencing (NGS) compatible primers specific to the genus Akkermansia were designed using this database. After optimization of amplification and library preparation steps for genus-specific next generation sequencing, gut microbiota samples from 64 PD patients [32 PDD and 32 PD with mild CI (PD-MCI)] and 26 HCs were analyzed by genus-specific amplicon sequencing. The results revealed the presence of seven strains assigned to Akkermansia muciniphila in gut microbiota samples, two of which showed significant distribution differences (p< 0.05) between demented (PDD) and non-demented groups (PD-MCI, HC). When gene contents of the detected Akkermansia genomes were examined through comparative genomic analysis, the presence of 12 genes only in Akkermansia genomes specific to non-demented groups were predicted. The annotations of these genes showed that they were not reported before with unknown functions. In this study, for the first time, gut microbiota samples from PD patients in Türkiye were analyzed using shotgun metagenomics, a novel genus-specific amplicon sequencing method was developed specifically for the analysis of Akkermansia genus, and then Akkermansia strains and genes potentially associated with CI stages in PD were identified using this method. The results underscore that investigating the species or strain level differences could help better understanding of the changes associated with PD in the human gut microbiota

Metaproteogenomic analysis of saliva samples from Parkinson's disease patients with cognitive impairment

Cognitive impairment (CI) is very common in patients with Parkinson's Disease (PD) and progressively develops on a spectrum from mild cognitive impairment (PD-MCI) to full dementia (PDD). Identification of PD patients at risk of developing cognitive decline, therefore, is unmet need in the clinic to manage the disease. Previous studies reported that oral microbiota of PD patients was altered even at early stages and poor oral hygiene is associated with dementia. However, data from single modalities are often unable to explain complex chronic diseases in the brain and cannot reliably predict the risk of disease progression. Here, we performed integrative metaproteogenomic characterization of salivary microbiota and tested the hypothesis that biological molecules of saliva and saliva microbiota dynamically shift in association with the progression of cognitive decline and harbor discriminatory key signatures across the spectrum of CI in PD. We recruited a cohort of 115 participants in a multi-center study and employed multi-omics factor analysis (MOFA) to integrate amplicon sequencing and metaproteomic analysis to identify signature taxa and proteins in saliva. Our baseline analyses revealed contrasting interplay between the genus Neisseria and Lactobacillus and Ligilactobacillus genera across the spectrum of CI. The group specific signature profiles enabled us to identify bacterial genera and protein groups associated with CI stages in PD. Our study describes compositional dynamics of saliva across the spectrum of CI in PD and paves the way for developing non-invasive biomarker strategies to predict the risk of CI progression in PD.FEMS Research and Training Gran

Association of HLA-DQ polymorphisms with Hepatitis B virus infection in Turkish population

Amaç Konak genetik faktörleri hepatit B virüs (HBV) enfeksiyonunun doğal seyri ve HBV ilişkili karaciğer hastalıklarının gelişme riski ile progresyonu üzerinde etkili olabilmektedir. Bu çalışmada HLA-DQ gen rs9272105, rs2856718 ve rs9275572 polimorfizmlerinin HBV doğal klirensi, viral yük ve HBV ile ilişkili karaciğer hasarı gelişimi ile ilişkisinin değerlendirilmesi amaçlanmıştır. Gereç ve Yöntem Çalışmaya 150 kronik hepatit B (KHB) hastası ile kontrol grubu olarak 58’i kronik hepatit C (KHC) ve 82’si farklı klinik endikasyonlar nedeniyle karaciğer biyopsi işlemi gerçekleştirilen 140 hasta dâhil edildi. HLA-DQ rs9272105, rs2856718 ve rs9275572 genotip ve polimorfizmlerinin belirlenmesinde TaqMan SNP genotiplendirme yöntemi kullanıldı. Bulgular KHB’li ve kontrol grubundaki hastaların HLA-DQ gen rs9272105, rs2856718 ve rs9275572 genotip ve allel frekansları arasında farklılık tespit edildi (P<0,05). HLA-DQ rs9272105 AA genotip ve A allel varlığı, hepatit B yüzey antijen (Hepatitis B surface antigen; HBSAg) klirensi ve karaciğer hasarı ile ilişkiliydi (p<0,05). HLA-DQ gen rs2856718 ve rs9275572 ise HBV klirensi ve hastaların histolojik sonuçlarıyla ve ayrıca rs9272105 de dâhil hastaların viral yükleriyle ilişkili değildi. Sonuç HLA-DQ rs9272105 AA genotip ve A allel gerek HBV enfeksiyonunun kronikleşmesi gerekse HBV ilişkili karaciğer hasarının gelişmesi için risk faktördür.Objective Host genetic factors can affect the natural course of hepatitis B virus (HBV) infection and the risk of development and progression of HBV-related liver diseases. The aim of this study is to evaluate the role of the HLA-DQ gene polymorphisms rs9272105, rs2856718 and rs9275572 with HBV natural clearance, viral load and the development of HBV associated liver injury. Materials and Methods The study included 150 patients with chronic hepatitis B (CHB) and 140 patients as the control group, 58 of whom had chronic hepatitis C (CHC) and 82 of whom had undergone a liver biopsy due to different clinical indications. The HLA-DQ gene rs9272105, rs2856718 and rs9275572 polymorphisms were genotypes in liver samples using the hybridization probe assay. Results A difference was found between the HLA-DQ gene rs9272105, rs2856718 and rs9275572 genotype and allele frequencies of the patients with CHB and the control group (P<0,05). The HLA-DQ rs9272105 AA genotype and presence of A allele were associated with hepatitis B surface antigen (HBsAg) clearance and liver injury (p<0,05). In contrast, the HLA-DQ genes rs2856718 and rs9275572 were not associated with HBV clearance and patients’ histological outcomes, nor with patients’ viral load, including rs9272105. Conclusions It has been suggested that the HLA-DQ rs9272105 AA genotype and the A allele are risk factors for both the persistence of HBV infection and the development of HBV-related liver damage

Microbial composition of Kombucha determined using amplicon sequencing and shotgun metagenomics

Kombucha, a fermented tea generated from the co-culture of yeasts and bacteria, has gained worldwide popularity in recent years due to its potential benefits to human health. As a result, many studies have attempted to characterize both its biochemical properties and microbial composition. Here, we have applied a combination of whole metagenome sequencing (WMS) and amplicon (16S rRNA and Internal Transcribed Spacer 1 [ITS1]) sequencing to investigate the microbial communities of homemade Kombucha fermentations from day 3 to day 15. We identified the dominant bacterial genus as Komagataeibacter and dominant fungal genus as Zygosaccharomyces in all samples at all time points. Furthermore, we recovered three near complete Komagataeibacter genomes and one Zygosaccharomyces bailii genome and then predicted their functional properties. Also, we determined the broad taxonomic and functional profile of plasmids found within the Kombucha microbial communities. Overall, this study provides a detailed description of the taxonomic and functional systems of the Kombucha microbial community. Based on this, we conject that the functional complementarity enables metabolic cross talks between Komagataeibacter species and Z. bailii, which helps establish the sustained a relatively low diversity ecosystem in Kombucha.Scientific Research Projects Coordination Unit of Istanbul Univ.Biotechnology and Biological Sciences Research Council (BBSRC)European Molecular Biology Laborator