Recent advances in molecular techniques to study microbial communities in food-associated matrices and processes

Justé, Annelies; Thomma, B.P.H.J.; Lievens, Bart

doi:10.1016/j.fm.2008.04.009

Cited by 176 publications

(126 citation statements)

References 232 publications

Supporting

Mentioning

122

Contrasting

Unclassified

Order By: Relevance

“…The detection and quantification of SSO can support and document efforts with good hygiene practices and thereby contribute to increasing quality and reducing product losses. In recent years, culture-independent molecular methods like real-time PCR have been increasingly applied to detect and quantify target microorganisms in food (36,37). Several real-time PCR methods have been developed to enumerate or detect pathogenic bacteria in seafood products, including Vibrio parahaemolyticus (26,38) and mesophilic Gram-negative histamine-producing bacteria (39,40).…”

Section: Discussionmentioning

confidence: 99%

Development of a Rapid Real-Time PCR Method as a Tool To Quantify Viable Photobacterium phosphoreum Bacteria in Salmon (Salmo salar) Steaks

Macé

Mamlouk

Chipchakova

et al. 2013

Appl Environ Microbiol

View full text Add to dashboard Cite

A specific real-time PCR quantification method combined with a propidium monoazide sample treatment step was developed to determine quantitatively the viable population of the Photobacterium phosphoreum species group in raw modified-atmospherepacked salmon. Primers were designed to amplify a 350-bp fragment of the gyrase subunit B gene (gyrB) of P. phosphoreum. The specificity of the two primers was demonstrated by using purified DNA from 81 strains of 52 different bacterial species. When these primers were used for real-time PCR in pure culture, a good correlation (R 2 of 0.99) was obtained between this method and conventional enumeration on marine agar (MA). Quantification was linear over 5 log units as confirmed by using inoculated salmon samples. On naturally contaminated fresh salmon, the new real-time PCR method performed successfully with a quantification limit of 3 log CFU/g. A correlation coefficient (R 2 ) of 0.963 was obtained between the PCR method and classic enumeration on MA, followed by identification of colonies (290 isolates identified by real-time PCR or by 16S rRNA gene sequencing). A good correlation with an R 2 of 0.940 was found between the new PCR method and an available specific conductance method for P. phosphoreum. This study presents a rapid tool for producing reliable quantitative data on viable P. phosphoreum bacteria in fresh salmon in 6 h. This new culture-independent method will be valuable for future fish inspection, the assessment of raw material quality in fish processing plants, and studies on the ecology of this important specific spoilage microorganism. Modified-atmosphere-packed (MAP) fresh fish is increasingly popular in Europe and widely sold in supermarkets as a chilled product. Compared to aerobically stored fresh fish, this kind of packaging, with typical headspace CO 2 concentrations of 20 to 60%, modifies the dominating microbiota mainly by reducing growth of aerobic Gram-negative bacteria like Pseudomonas (1, 2). This results in an extended shelf life which facilitates the chilled distribution and marketing of fresh MAP fish. However, this packaging allows the growth of CO 2 -resistant bacteria, including Gram-positive lactic acid bacteria and the Gram-negative bacterium Photobacterium phosphoreum (2-4). The latter has been identified as the specific spoilage organism (SSO) responsible for trimethylamine production and sensory spoilage of MAP cod (5, 6) and as the main spoilage bacterial species of several chilled marine fish, including cod, garfish, halibut, saithe, salmon, and shrimp (7-15).Multilocus analysis, based on 16S rRNA and gyrB and luxABFE genes, divided strains originally isolated and identified as P. phosphoreum into three distinct clades of P. phosphoreum, Photobacterium iliopiscarium, and Photobacterium kishitanii (16,17). The members of the P. phosphoreum species group have been reported as important for spoilage of raw MAP fish, and they include both luminous and nonluminous variants (5, 18). It is therefore relevant to detect and enumerate this s...

show abstract

Section: Discussionmentioning

confidence: 99%

Development of a Rapid Real-Time PCR Method as a Tool To Quantify Viable Photobacterium phosphoreum Bacteria in Salmon (Salmo salar) Steaks

Macé

Mamlouk

Chipchakova

et al. 2013

Appl Environ Microbiol

View full text Add to dashboard Cite

show abstract

“…Soil microbial rRNA gene were amplified using primer sets containing the Roche 454 pyrosequencing adaptors (underlined), which followed bacterial primer set (5 ′ -CGTATCGCCTCCCTCGCGCCATCAGbarcode-AGAGTTTGATCMTGGCTCAG-3 ′ and 5 ′ -CTAT GCGCCTTGCCAGCCCGCTCAG-GTATTACCGCGGCTGC TGGCAC-3 ′ ) (Justé et al, 2008), archaeal set (5 ′ -TTTTCT ATGCGCCTTGCCAGCCCGCT-CAGCAGCMGCCGCGGTA A-3 ′ and 5 ′ -CGTATCGCCTCCCTCGCGCCATCAG-barcode-GGCCATGCACCWCCTCTC-3 ′ ) (Kolganova et al, 2002), and fungal set (5 ′ -CGTATCGCCTCCCTCGCGCCATCAGbarcode-CAGTAGTCATATGCTTGTCTC-3 ′ and 5 ′ -CTATGC GCCTTGCCAGCCCGCTCAG-GCTGCTGGCACCAGACTT GC-3 ′ ) (Costa et al, 2006). There were 7-, 10-, and 10-base barcodes for primers of bacteria, archaea, and fungi, respectively.…”

Section: Rna Genetic Pyrosequencingmentioning

confidence: 99%

The Effects of Various Land Reclamation Scenarios on the Succession of Soil Bacteria, Archaea, and Fungi Over the Short and Long Term

Liu

Chen

2016

Front. Ecol. Evol.

View full text Add to dashboard Cite

Ecological restoration of mining areas has mainly focused on the succession dynamics of vegetation and the fate of microbial communities remains poorly understood. We examined changes in soil characteristics and plant and microbial communities with increasing reclamation period in an open coal mine. Bacterial, archaeal and fungal communities were assessed by tag-encoded 454 pyrosequencing. At the phylum level, Proteobacteria, Crenarchaeota, and Ascomycota had the highest detected relative abundance within bacteria, archaea, and fungi, respectively. Partial regressions and canonical correspondence analysis demonstrated that vegetation played a major role in bacterial and archaeal diversity and assemblies, and soil characteristics, especially nitrogen, were important for fungal diversity and assemblies. Spearman rank correlation indicated that bacterial and archaeal communities showed synergistic succession with plants; whereas, fungal communities showed no such pattern. Overall, our data suggest that there are different drivers of bacterial, archaeal and fungal succession during secondary succession in a reclaimed open mine.

show abstract

“…Ezért a vizsgálandó minta határérté-ket jelentő mennyiségében (például 1 vagy 25 ml, illetve gramm) a kimutatandó mikrobát a PCR-reakció előtt dúsító közeg segítségével felszaporítják olyan sejtszámra, amiből már a PCR-es vizsgálathoz megfelelő mennyisé-gű templát-DNS (vagy RNS) izolálható [9]. Ennek kö-vetkeztében a pozitív PCR-reakció határérték feletti, míg a negatív határérték alatti mikrobaszámot jelez a mintában (úgynevezett jelenlét vagy hiány kimutatása [10]).…”

Section: Pcr-alapú Módszerek Alkalmazása éLelmiszer-biztonsági Jelentunclassified

Élelmiszer-biztonsági jelentőségű baktériumok molekuláris detektálásának fejlesztése miniatürizált mikrofluidikai eszközök segítségével

Iván

Maráz

2015

Orvosi Hetilap

View full text Add to dashboard Cite

A biztonságos élelmiszerek előállítása szempontjából kulcsfontosságú az élelmiszerrel terjedő patogén baktériumok kimutatása és azonosítása. A hagyományos, tenyésztésen alapuló diagnosztikai eljárásokat egyre inkább felváltják vagy kiegészítik a nukleinsav-alapú, a genom speciális (elsősorban virulencia) génjeinek kimutatását célzó molekuláris technikák. A rutin élelmiszer-mikrobiológiai vizsgáló laboratóriumok leggyakrabban nemzetközileg validált DNSamplifi kációs, elsősorban valós idejű polimeráz láncreakció alapú módszereket alkalmaznak, amelyek a vizsgálati idő jelentős lerövidítése mellett lényegesen javítják a módszerek teljesítési jellemzőit (például érzékenység, specifi kusság) is. A polimeráz láncreakció alapú módszereknek rutindiagnosztikai célú alkalmazása azonban az előnyök mellett szá-mos hátránnyal is jár, amelyek között említendő a készülékek és a reagensek magas költsége, valamint a laboratóriumi környezetnek a reakciótermékekkel való kontaminálási kockázata, ami elkülönített laboratóriumi rendszert igényel. Manapság az ilyen laboratóriumi rendszerek miniatürizálása és hordozhatóvá tétele is fontos fejlesztési irány. A Labon-a-chip eszközökben több ilyen laboratóriumi műveletet lehet megvalósítani egy kis méretű eszközön, a standard eljárásokhoz hasonló pontossággal és megbízhatósággal. Ezen miniatürizált eszközök nagy előnye az egyszerű -sokszor automatizált -kezelhetőség, kis méret, hordozhatóság és sterilitás, ami az egyszeri használatból adódik. Ilyen miniatürizált gyorsdiagnosztikai eszközök kutatása és fejlesztése folyik a világ vezető kutatóhelyein, például különbö-ző minta-előkészítési és DNS-amplifi kációs módszerek miniatürizálásával. A szerzők is ezt a célt tűzték ki kutatásaik-ban: olyan miniatürizált mikrofl uidikai eszközök fejlesztését, amelyek alkalmasak élelmiszer-biztonsági jelentőségű baktériumok molekuláris detektálására. Orv. Hetil., 2015, 156(51), 2082-2088.Kulcsszavak: élelmiszer-biztonság, baktériumdiagnosztika, Lab-on-a-chip, mikrofl uidikai eszközök Development of molecular detection of food-borne pathogenic bacteria using miniaturized microfl uidic devicesDetection and identifi cation of food-borne pathogenic bacteria are key points for the assurance of microbiological food safety. Traditional culture-based methods are more and more replaced by or supplemented with nucleic acid based molecular techniques, targeting specifi c (preferably virulence) genes in the genomes. Internationally validated DNA amplifi cation -most frequently real-time polymerase chain reaction -methods are applied by the food microbiological testing laboratories for routine analysis, which will result not only in shortening the time for results but they also improve the performance characteristics (e.g. sensitivity, specifi city) of the methods. Beside numerous advantages of the polymerase chain reaction based techniques for routine microbiological analysis certain drawbacks have to be mentioned, such as the high cost of the equipment and reagents, as well as the risk of contamination of the labora...

show abstract

Recent advances in molecular techniques to study microbial communities in food-associated matrices and processes

Cited by 176 publications

References 232 publications

Development of a Rapid Real-Time PCR Method as a Tool To Quantify Viable Photobacterium phosphoreum Bacteria in Salmon (Salmo salar) Steaks

Development of a Rapid Real-Time PCR Method as a Tool To Quantify Viable Photobacterium phosphoreum Bacteria in Salmon (Salmo salar) Steaks

The Effects of Various Land Reclamation Scenarios on the Succession of Soil Bacteria, Archaea, and Fungi Over the Short and Long Term

Élelmiszer-biztonsági jelentőségű baktériumok molekuláris detektálásának fejlesztése miniatürizált mikrofluidikai eszközök segítségével

Contact Info

Product

Resources

About