Integration of Meta-Multi-Omics Data Using Probabilistic Graphs and External Knowledge

Multi-omics has the promise to provide a detailed molecular picture of biological systems. Although obtaining multi-omics data is relatively easy, methods that analyze such data have been lagging. In this paper, we present an algorithm that uses probabilistic graph representations and external knowledge to perform optimal structure learning and deduce a multifarious interaction network for multi-omics data from a bacterial community. Kefir grain, a microbial community that ferments milk and creates kefir, represents a self-renewing, stable, natural microbial community. Kefir has been shown to have a wide range of health benefits. We obtained a controlled bacterial community using the two most abundant and well-studied species in kefir grains: Lentilactobacillus kefiri and Lactobacillus kefiranofaciens. We applied growth temperatures of 30 °C and 37 °C and obtained transcriptomic, metabolomic, and proteomic data for the same 20 samples (10 samples per temperature). We obtained a multi-omics interaction network, which generated insights that would not have been possible with single-omics analysis. We identified interactions among transcripts, proteins, and metabolites, suggesting active toxin/antitoxin systems. We also observed multifarious interactions that involved the shikimate pathway. These observations helped explain bacterial adaptation to different stress conditions, co-aggregation, and increased activation of L. kefiranofaciens at 37 °C.

Determining the aflatoxin M1 levels in breast milk

OBJECTIVE

Mycotoxins are different toxic substances at relatively smaller molecular weight produced by some types of fungi. Aflatoxin is the most common type of mycotoxin easily reproducing in food stored for a long time in unsuitable conditions. This study determined the aflatoxin M1 (AFM1) levels in breast milk samples collected from mothers who gave birth in Kırşehir, Turkey.

MATERIALS AND METHODS

A total of 82 breast milk samples to be analyzed to determine the AFM1 levels were collected from voluntary breastfeeding mothers who gave birth in the Kırşehir Training and Research Hospital and who were randomly selected. The AFM1 levels were determined using the competitive ELISA kit.

RESULTS

The AFM1 levels in the breast milk samples of mothers who did not consume milk were lower than those of other mothers. The AFM1 levels in the breast milk samples of mothers consuming fabrication milk were lower than mothers consuming homemade milk (p<0.01). Additionally, the AFM1 levels in the breast milk samples of mothers consuming homemade or self-made bread were lower (p<0.05).

CONCLUSIONS

This study found that the nutritional habits of breastfeeding mothers affected the AFM1 levels in breast milk.

Growth of Trichomonas vaginalis in Basic Media Available in Routine Microbiology Laboratories

OBJECTIVE

Trichomonas vaginalis is a protozoan parasite with unicellular, flagellate, and anaerobic metabolism. It is the second most prevalent pathogen among sexually transmitted agents after viruses. Microscopic examination, culture, and molecular methods are used in the laboratory diagnosis of T. vaginalis. However, in most routine microbiology laboratories, microscopy is preferred instead of culture and molecular methods for T. vaginalis diagnosis because microscopy is cheaper than other methods. This study aimed to produce T. vaginalis in media that can be detected frequently in microbiology laboratories.

METHODS

In this study, four media, namely, thioglucholate medium (THIO), brain heart infusion medium (BHI), tryptic soy broth medium (TSB), and Brucella broth medium (BRB) were modified and tested. Trypticase-yeast extract-maltose (TYM) medium was used as a reference medium. Each medium tested was enriched with three different serum additives. T. vaginalis trophozoite at a density of 10⁴ parasites/mL was inoculated into each medium and incubated at 37 °C for 10 days. We determined the number of trophozoites using a hemocytometer, and the viability rates were determined using trypan blue.

RESULTS

Trichomonas vaginalis grew extremely well on THIO, BHI, and TSB media but not on BRB media. The time and number of parasites peaked were determined as 100×10⁴ parasites/mL on THIO-ATS and THIO-FCS media on days five and four, respectively, 100×10⁴ parasites/mL on BHI-ATS on day three, 98×10⁴ parasite/mL on BHI-FCS media on day five, 100×10⁴ parasites/mL on TSB-ATS on day four, and 82×10⁴ parasite/mL on TSB-FCS media on day seven. Compared with the reference medium, TYM, T. vaginalis trophozoites survived significantly longer in THIO, BHI, and TSB media.

CONCLUSION

The rich content of THIO, TSB, and BHI media, which are widely available in routine microbiology laboratories, may allow T. vaginalis growth.

In-vitro GIT Tolerance of Microencapsulated Bifidobacterium bifidum ATCC 35914 Using Polysaccharide-Protein Matrix

Longevity of probiotic is the main concern for getting maximum benefits when added in food product. Bifidobacterium, a probiotic, tends to lose its viability during gastrointestinal track (GIT) transit and storage of food. Their viability can be enhanced through microencapsulation technology. In this study, Bifidobacterium bifidum (B. bifidum) ATCC 35914 was encapsulated by using two experimental plans. In the first plan, chitosan (CH) at 0.6, 0.8, and 1.0% and sodium alginate (SA) at 4, 5, and 6% were used. Based on encapsulation efficiency, 6% sodium alginate and 0.8% chitosan were selected for single coating of the bacteria, and the resulting micro beads were double coated with different concentrations (5, 7.5, and 10%) of whey protein concentrate (WPC) in the second plan. Encapsulation efficiency and GIT tolerance were determined by incubating the micro beads in simulated gastrointestinal juices (SIJ) at variable pH and exposure times, and their release (liberation of bacterial cells) profile was also observed in SIJ. The microencapsulated bacterial cells showed significantly (P < 0.01) higher viability as compared to the unencapsulated (free) cells during GIT assay. The double-coated micro beads SA 6%-WPC 5% and CH 0.8%-WPC 5% were proven to have the higher survival at pH 3.0 after 90 min of incubation time and at pH 7.0 after 3-h exposure in comparison to free cells in simulated conditions of the stomach and intestine, respectively. Moreover, double coating with whey protein concentrate played a significant role in the targeted (10^6-9 CFU/mL) delivery under simulated intestinal conditions.

Thermal and Starvation Stress Response of Escherichia coli O157:H7 Isolates Selected from Agricultural Environments

Pathogens exposed to agricultural production environments are subject to multiple stresses that may alter their survival under subsequent stress conditions. The objective of this study was to examine heat and starvation stress response of Escherichia coli O157:H7 strains isolated from agricultural matrices. Seven E. coli O157:H7 isolates from different agricultural matrices-soil, compost, irrigation water, and sheep manure-were selected, and two ATCC strains were used as controls. The E. coli O157:H7 isolates were exposed to heat stress (56°C in 0.1% peptone water for up to 1 h) and starvation (in phosphate-buffered saline at 37°C for 15 days), and their survival was examined. GInaFiT freeware tool was used to perform regression analyses of the surviving populations. The Weibull model was identified as the most appropriate model for response of the isolates to heat stress, whereas the biphasic survival curves during starvation were fitted using the double Weibull model, indicating the adaptation to starvation or a resistant subpopulation. The inactivation time during heating to achieve the first decimal reduction time (δ) calculated with the Weibull parameters was the highest (45 min) for a compost isolate (Comp60A) and the lowest (28 min) for ATCC strain 43895. Two of the nine isolates (ATCC 43895 and a manure isolate) had β < 1, indicating that surviving populations adapted to heat stress, and six strains demonstrated downward concavity (β > 1), indicating decreasing heat resistance over time. The ATCC strains displayed the longest δ₂ (>1,250 h) in response to starvation stress, compared with from 328 to 812 h for the environmental strains. The considerable variation in inactivation kinetics of E. coli O157:H7 highlights the importance of evaluating response to stress conditions among individual strains of a specific pathogen. Environmental isolates did not exhibit more robust response to stress conditions in this study compared with ATCC strains.

Intravital microscopic evaluation of cremasteric microcirculation in experimental testicular torsion

AIM

Although absent cremasteric reflex is a significant clinical finding for testicular torsion (TT), there is limited information about microcirculation of the cremasteric muscle (CM) after TT. This experimental study was performed to evaluate CM microcirculation by intravital microscopy after TT.

MATERIALS AND METHODS

Twelve Wistar rats were allocated into two equal groups: control (CG) and torsion (TG). After anesthetization of the CG rats, the CM flap was dissected through a left ventral inguinal incision with its vascular pedicle. In TG rats, TT was performed by rotating left testicles 720(°) in clockwise direction for 1 h. Then, the CM flap was dissected as in CG, and was placed under an intravital microscope. Vessel diameters, functional capillary perfusion and leukocyte activation in post-capillary venules were measured and evaluated statistically.

RESULTS

There was a significant decrease in vessel diameter in TG compared to CG (p < 0.05). The median of perfused capillaries in CG and TG was 13 (11.75-14.30) and 5.5 (4.75-7.25), respectively (p < 0.05). Number of granulocytes (rolling, sticking, transmigrated) was greater in TG than CG (p < 0.05).

CONCLUSION

Intravital microscopic evaluation of CM after TT showed decrease in vessel diameter and number of perfused capillaries, and increase in granulocyte activation. Clinical, electrophysiological alterations in CM after TT can be explained by deterioration of microcirculation of CM.