The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.

SPAdes, a new genome assembly algorithm and its applications to single-cell sequencing ( 7th Annual SFAF Meeting, 2012)

Manual for the Identification of Medical Bacteria.

http://academic.oup.com/milmed/article-pdf/146/1/60/24125826/milmed-146-1-60.pdf

Biochemical Tests for Identification of Medical Bacteria

Pickling C. botulinumtoxin formation in finished product Maximum finished product pH in the loin muscle of 5.0 Finished product pH in the loin muscle Collect sample of product from each pickling tank at the end of each pickling cycle and analyze for pH using a pH meter Each pickling tank, each cycle QC personnel Continue pickling process until pH meets the CL Analytical results Daily calibration of pH meter

Food and Drug Administration Center for Food Safety and Applied Nutrition

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Basic Laboratory Procedures In Clinical Bacteriology

A grand total of 150 random samples of fresh water fish (Tilapia nilotica), marine water fish (Mugilcephalus), and farm water fish (Tilapia nilotica) fish (50 of each) were collected from Sharkia governorduring summer of 2014 to investigate the incidence of Vibrio spp. as well as studying the effect of heattreatments (frying and roasting). The obtained results revealed that incidence of Vibrio spp. in freshwater fish were 13 (26%)‚ the overall incidence in the samples was 4(8%) for V. vulnificus, and 2(4%),2(4%), 2(4%), 2(4%) and 1(2%) for, V. mimicus, V. fluvialis, V. damsel, V. furnissi, and V. alginolyticus,respectively. In marine fish Vibrio spp. were 24(48%), the overall incidence in the samples was for V.parahaemolyticus 5(10%), V. vulnificus 4(8%), V. fluvialis4 (8%), V. mimicus 7(14%), V. alginolyticus2(4%), and V. damsel 2(4%). In farm water fish Vibrio spp. were 17(34%) while the overall incidencein the samples was V. parahaemolyticus 1(2%), V. vulnificus 3(6%), V. fluvialis 3(6%), V. mimicus5(10%), V. alginolyticus 2(4%), and V. damsela 3(6%). Ten pieces of fish fillet (100g of each and 5pieces for each treatment) were used to study the effect of frying with cotton seed oil (1900 C) for 10minutes and roasting in oven at 1500C for 10 minutes after their inoculation with 106 cfu/g V.paraheamolyticus. After roasting and frying‚ the microbial counts of V. paraheamolyticus weredecreased by 98.2% and 100%, respectively.

https://bvmj.journals.ekb.eg/article_31788_dd2fc20b2fdec7e6d85a37248c754912.pdf

Incidence of Vibrio species in fish with special emphasis on the effect of heat treatments

A total of 180 Oreochromis niloticus and 120 Clarias gariepenus of different weight and length were randomly collected from three different markets (El-Moneib, El-Ayiat and El-Badrashin) in Giza Governorate from January to June 2012. Muscles and organs of the fishes were examined for infective zoonotic parasites. The total prevalence of encysted metacercariae (EMC) among examined O. niloticus was 82.8%, the highest prevalence was in the tail (75%), while the lowest one (17%) in skin, and in the gills was (57.2%). Total prevalence of EMC was 35.8% in the C. gariepenus, the highest was in trunk (27.5%), then head & tail (25.8% &25%) and the lowest one (4.1%) was in the skin but none in the gills. There was an indirect relationship between the EMC prevalence and the fishes weight and length. The recovered EMC from O. niloticus were; Diplostomatidae, Cyathocotylide and Heterophyidae. Besides, Cyanodiplostomatidae and Cyathocotylide were recovered from C. gariepenus. These EMC were successfully developed to adults after experimental infection to pigeons and rats. The emerging adult flukes were Prohemistomum vivax, Mesostephanus appendiculatus and Centrocetus armatus.

https://jesp.journals.ekb.eg/article_68295_8fd9b58bb0c4f2f560200cd530b06931.pdf

Prevalence of metacercarial infection in some marketed fish in giza governorate, egypt

This work was carried out to evaluate the fungal quality of basterma and minced meat sold in localmarkets in as well as to evaluate the use of essential oil of clove and Cinnamon essential oil as antifungalagent (in vivo) in food preservation. The total mould counts in the examined samples ranged from 2.0to 3.6 log cfu/g with a mean value of 2.9 log cfu/g for basterma, while the mean count in minced meatwas 2.4 log cfu/g and ranged from 0.6 to 3.2 log cfu/g. While the total yeast counts in the examinedmeat samples ranged from 1.7 to 2.4 log cfu/g, with a mean value of 2.1 log cfu/g for basterma, whilethat in minced meat was 2.9 log cfu/g and ranged from 2.4 to 3.1 log cfu/g. In the examined samples, 9mould and 3 yeast genera were identified. Minced meat used in these trials was treated with 0.5 %, 1%and 1.5% from each essential oil. The obtained results showed that the tested essential oils caused ahighly significant inhibition on fungal growth. Clove oil (1.5 %) was needed for inhibition of yeast andmould growth. The authors concluded that these essential oils have the potential to be used in food asflavoring and natural preservatives. Thus, the essential oil of clove and cinnamon could be used tocontrol food spoilage as a potential source of food preservative. The antifungal effects of clove oil werefound to be more effective than those of cinnamon oil, but the odour of cinnamon is more palatable thanthe clove odour

https://bvmj.journals.ekb.eg/article_31797_9cc91e6a0e77482d28ab4befeaa026fc.pdf

The using of essential oils in improving mycological status of some meat products

Plant essential oils (EOs) serve as a “safe” alternative to chemical or synthetic antimicrobials and antioxidants to struggle with the food borne pathogens or spoilage organisms, inhibiting lipid oxidation so, the effect of some essential oils as thyme (thymus vulgaris), cinnamon (cinnamomum zeylanicum) and garlic (Allium sativum) at concentrations (1%) as natural preservatives as well as their ability to increase the shelf life of minced meat, and also their effects on bacterial agents as Staphylococcus aureus and E. coli and sensory properties of minced meat after 3 hrs, 1st, 2nd, 3rd, 4th and 5th day during cold storage at 4°C. The obtained results showed that treated samples revealed decreasing values of S. aureus and E. coli counts and improving sensory properties than untreated samples (control) ones. Also, thyme oil at concentration (1%) was more effective than cinnamon and garlic oils.

Antimicrobial Effect of Some Essential Oils on Some Pathogenic Bacteria in Minced Meat

One Hundered randam samples of different meat products represented by (rice kofta, kobaba, sausage and beef burger) were collected randomly from different supermarkets in Kalyobia governorates to be examined for occurance of B. Cereus & its virulence genes. The incidence of Bacillus Cereus was 60%, 52%, 40% & 36% for rice kofta, kobeba, sausage and beef burger, respectively.  Moreover, the results of PCR out of 47 of isolated B. Cereus from the examined samples of meat prouducts were 15(31.91%) for cytk, 7(14.89%) for hblc and cytk & hblc 24(51.6%), respectively. Public Health significance of B. Cereus and its virulence genes and possible sources of meat product contamination as well as some recommendations to improve the quality of meat products were discussed

https://bvmj.journals.ekb.eg/article_44351_6de9cdcb015f52604fc1da494ba1bf24.pdf

Saad M. Saad

Papers

Incidence of Vibrio species in fish with special emphasis on the effect of heat treatments

Prevalence of metacercarial infection in some marketed fish in giza governorate, egypt

The using of essential oils in improving mycological status of some meat products

Antimicrobial Effect of Some Essential Oils on Some Pathogenic Bacteria in Minced Meat

Occurrence of Bacillus Cereus and its Virulence genes in Some Meat Products by Multiplex PCR