Advances in genomics for microbial food fermentations and safety

The exponentially growing collection of genomic sequence information, the high-throughput analysis of expression products, and the ability to order this information using advanced bioinformatics are expected to affect biotechnology and life sciences in a profound and unprecedented way. These developments offer many possibilities to improve the functionality of fermentations by food-grade microorganisms and to increase the microbial safety of foods. It will be necessary to combine functional studies with comparative genomics approaches to provide effective strategies for improving the functionality and safety of foods.     

Next-generation sequencing and its potential impact on food microbial genomics

Recent efforts of researchers to elucidate the molecular mechanisms of biological systems have been revolutionized greatly with the use of high throughput and cost-effective techniques such as next generation sequencing (NGS). Application of NGS to microbial genomics is not just limited to predict the prevalence of microorganisms in food samples but also to elucidate the molecular basis of how microorganisms respond to different food-associated conditions, which in turn offers tremendous opportunities to predict and control the growth and survival of desirable or undesirable microorganisms in food. Concurrently, NGS has facilitated the development of new genome-assisted approaches for correlating genotype and phenotype. The aim of this review is to provide a snapshot of the various possibilities that these new technologies are opening up in area of food microbiology, focusing the discussion mainly on lactic acid bacteria and yeasts associated with fermented food. The contribution of NGS to a system level understanding of food microorganisms is also discussed.     

Bacteriophage ecology in commercial sauerkraut fermentations

Knowledge of bacteriophage ecology in vegetable fermentations is essential for developing phage control strategies for consistent and high quality of fermented vegetable products. The ecology of phages infecting lactic acid bacteria (LAB) in commercial sauerkraut fermentations was investigated. Brine samples were taken from four commercial sauerkraut fermentation tanks over a 60- or 100-day period in 2000 and 2001. A total of 171 phage isolates, including at least 26 distinct phages, were obtained. In addition, 28 distinct host strains were isolated and identified as LAB by restriction analysis of the intergenic transcribed spacer region and 16S rRNA sequence analysis. These host strains included Leuconostoc, Weissella, and Lactobacillus species. It was found that there were two phage-host systems in the fermentations corresponding to the population shift from heterofermentative to homofermentative LAB between 3 and 7 days after the start of the fermentations. The data suggested that phages may play an important role in the microbial ecology and succession of LAB species in vegetable fermentations. Eight phage isolates, which were independently obtained two or more times, were further characterized. They belonged to the family Myoviridae or Siphoviridae and showed distinct host ranges and DNA fingerprints. Two of the phage isolates were found to be capable of infecting two Lactobacillus species. The results from this study demonstrated for the first time the complex phage ecology present in commercial sauerkraut fermentations, providing new insights into the bioprocess of vegetable fermentations.     

Linkage of microbial ecology to phenotype: correlation of rumen microbial ecology to cattle's feed efficiency

Linkage of rumen microbial structure to host phenotypical traits may enhance the understanding of host-microbial interactions in livestock species. This study used culture-independent PCR-denaturing gradient gel electrophoresis (PCR-DGGE) to investigate the microbial profiles in the rumen of cattle differing in feed efficiency. The analysis of detectable bacterial PCR-DGGE profiles showed that the profiles generated from efficient steers clustered together and were clearly separated from those obtained from inefficient steers, indicating that specific bacterial groups may only inhabit in efficient steers. In addition, the bacterial profiles were more likely clustered within a certain breed, suggesting that host genetics may play an important role in rumen microbial structure. The correlations between the concentrations of volatile fatty acids and feed efficiency traits were also observed. Significantly higher concentrations of butyrate (P < 0.001) and valerate (P = 0.006) were detected in the efficient steers. Our results revealed potential associations between the detectable rumen microbiota and its fermentation parameters with the feed efficiency of cattle.     

Impact of a synbiotic food on the gut microbial ecology and metabolic profiles

Background  

The human gut harbors a diverse community of microorganisms which serve numerous important functions for the host wellbeing. Functional foods are commonly used to modulate the composition of the gut microbiota contributing to the maintenance of the host health or prevention of disease. In the present study, we characterized the impact of one month intake of a synbiotic food, containing fructooligosaccharides and the probiotic strains Lactobacillus helveticus Bar13 and Bifidobacterium longum Bar33, on the gut microbiota composition and metabolic profiles of 20 healthy subjects.     

Marine viral ecology: incorporation of bacteriophage into the microbial planktonic food web paradigm

In the decade since the microbial loop was defined by Azam etat. (Mar. Ecol. Prog. Ser., 59, 1–17, 1983), the importanceof the interaction between microbial organisms and the largerplanktonic animals has been a subject of controversy. Untilrecently, grazing was considered to be the major fate of bacterialproduction. Now, however, viruses are seen to have an importantrole in microbial processes. We describe how growth and recyclingparameters affect the transfer of bacterial production througha microbial loop model that includes viruses. The loop is veryinefficient for all reasonable conditions, but its relativeimportance as a source of mesozooplankton nutrition is variable.The model demonstrates that in mesotrophic coastal waters, themicrobial loop is unlikely to supply more than a minor componentof mesozooplankton nutrition, a proposition that is supportedby accumulating evidence. For oligotrophic pelagic waters, themodel indicates that in the absence of viruses the microbialloop, despite its low efficiency, may provide an important resourcefor mesozooplankton. Bacterial production, without viral mortality,is also relatively important in the case of direct exploitationby salps. Under these conditions, bacteria account for 10–30%of mesozooplankton nutrition. With high levels of bacteriophageactivity, zooplankton production is generally reduced by 5–15%.We thus conclude that bactenophages could significantly affectmesozooplanktonic and, hence, exploitable marine production. ¹Present address: CSIRO Division of Fisheries, GPO Box 1538,Hobart, Tasmania 7001, Australia ²Present address: Resource Protection Division, Parks and WildlifeDepartment, 3000 1H 35 South, Suite 320, Austin, TX 78704, USA     

Relevance of microbial coculture fermentations in biotechnology

The purpose of this article is to review coculture fermentations in industrial biotechnology. Examples for the advantageous utilization of cocultures instead of single cultivations include the production of bulk chemicals, enzymes, food additives, antimicrobial substances and microbial fuel cells. Coculture fermentations may result in increased yield, improved control of product qualities and the possibility of utilizing cheaper substrates. Cocultivation of different micro‐organisms may also help to identify and develop new biotechnological substances. The relevance of coculture fermentations and the potential of improving existing processes as well as the production of new chemical compounds in industrial biotechnology are pointed out here by means of more than 35 examples.     

Traditional food fermentations as industrial resources

Asia is rich in resources which can contribute widely to food processing and production over the next 207–50 years as world population reaches 6 billion. The world needs low cost methods of providing nutritious proteinrich meat analogues for its thousands of millions of consumers. The Indonesian tempe fermentation will serve as a model. A bacterium present in commercial tempe can be used to add vitamin B-12 to other vegetarian foods. Fuel requirements for cooking can be decreased by applying a fungal fermentation of the tempe/ontjom type to legume substrates. The world needs high quality meat-flavors derived from vegetable protein. The soy sauce (kecap)/miso (tauco) processes and the fish/shrimp sauce and paste processes can be modified to yield a wide variety of meat-like flavors for use in formulating new foods. The protein content of high starch substrates can be increased by applying the Indonesian tape fermentation. Leavened sour-dough bread-like products can be produced without the use of wheat or ryeflours using the Indian idli/dosai fermentation. Coconut protein, if extracted without denaturing, can serve as a valuable base for a new type of puddings and related foods. Finally Asia is an almost endless source of cultures of edible microorganisms that, with further study of their synthetic abilities, particularly regarding amino acids and vitamins, could lead to new industries.     

Evolutionary engineering to enhance starter culture performance in food fermentations

1. Download : Download high-res image (199KB)
2. Download : Download full-size image