A Vegetable Fermentation Facility Hosts Distinct Microbiomes Reflecting the Production Environment

Abstract

Fermented vegetables are highly popular internationally in part due to their enhanced nutritional properties, cultural history, and desirable sensorial properties. In some instances, fermented foods provide a rich source of the beneficial microbial communities that could promote gastrointestinal health. The indigenous microbiota that colonize fermentation facilities may impact food quality, food safety, and spoilage risks and maintain the nutritive value of the product. Here, microbiomes within sauerkraut production facilities were profiled to characterize variance across surfaces and to determine the sources of these bacteria. Accordingly, we used high-throughput sequencing of the 16S rRNA gene in combination with whole-genome shotgun analyses to explore biogeographical patterns of microbial diversity and assembly within the production facility. Our results indicate that raw cabbage and vegetable handling surfaces exhibit more similar microbiomes relative to the fermentation room, processing area, and dry storage surfaces. We identified biomarker bacterial phyla and families that are likely to originate from the raw cabbage and vegetable handling surfaces. Raw cabbage was identified as the main source of bacteria to seed the facility, with human handling contributing a minor source of inoculation. and dominated all surfaces where spontaneous fermentation occurs, as these taxa are associated with the process. Wall, floor, ceiling, and barrel surfaces host unique microbial signatures. This study demonstrates that diverse bacterial communities are widely distributed within the production facility and that these communities assemble nonrandomly, depending on the surface type. Fermented vegetables play a major role in global food systems and are widely consumed by various global cultures. In this study, we investigated an industrial facility that produces spontaneous fermented sauerkraut without the aid of starter cultures. This provides a unique system to explore and track the origins of an "in-house" microbiome in an industrial environment. Raw vegetables and the surfaces on which they are handled were identified as the likely source of bacterial communities rather than human contamination. As fermented vegetables increase in popularity on a global scale, understanding their production environment may help maintain quality and safety goals.

The International Scientific Association for Probiotics and Prebiotics (ISAPP) consensus statement on fermented foods

“…Culture-dependent methods remain the gold standard for the strain-level characterization of fermentation microbiota; however, these methods are increasingly complemented by holistic, meta-omics methods (metagenomics, metatranscriptomics, metaproteomics and metabolomics) 55 . Molecular approaches have shown that fermented foods are frequently dependent on complex, multi-kingdom, microbial communities functioning in concert via dynamic succession processes [56][57][58][59] . However, despite this complexity, the presence of a so-called core microbiota (defined as widespread microorganisms that are central to the functions of these ecosystems) are often apparent in a wide range of fermented foods [60][61][62][63][64] .…”

Establishment Limitation Constrains the Abundance of Lactic Acid Bacteria in the Napa Cabbage Phyllosphere

“…Culture-based studies from the 1960s noted that LAB are in low abundance on the surfaces of cucumbers, beets, carrots, and other vegetables (67). A recent survey of a fermentation production facility found that LAB are in low levels in the green cabbage phyllosphere (49). Collectively, these studies demonstrate a consistently low abundance of LAB across other species and varieties of cabbage, as well as other vegetables.…”

“…Sequence-based data on cabbage phyllosphere bacterial diversity are very limited (43,49), and our amplicon sequence data help fill this gap. Across the three sites, Proteobacteria dominated the amplicon sequence data sets, with Bacteroidetes, Firmicutes (non-LAB), and Actinobacteria making up smaller fractions of the NCP at each site (Fig.…”

Stochasticity in microbiology: managing unpredictability to reach the Sustainable Development Goals

“…Many other food products, such as salami, sauerkraut, sourdough, surströmming and hákarl, wine, cheese, yoghurt and kefir, all rely on microbiomes for flavour, odour, texture and even shelf life. In vegetable fermentation facilities that produce spontaneously fermented sauerkraut, the raw vegetables and indoor environment and surfaces hosted distinct microbiomes, which were reflected in the final product (Einson et al , 2018). In contrast, human contamination was found to have no effect on the final product.…”