Multi-omics approaches to elucidate the role of interactions between microbial communities in cheese flavor and quality

Effect of L. Plantarum Y279 and W. Cibaria Y113 on microorganism, lipid oxidation and fatty acid metabolites in Yu jiaosuan, A Chinese tradition fermented snack

Fatty acids are one of the main sources of flavour in fermented Yu jiaosuan (YJS) in southwest China. Bacilli (50.18 %) and Oxyphotobacteria (32.70 %) were the dominant class. Lactiplantibacillus (40.51 %) and Weissella (20.43 %) were the dominant species in the inoculated fermented group (HY). The peroxide value (ZY: 0.025 g/100 g, HY: 0.016 g/100 g) and lipoxygenase (LOX) (ZY: 5.7654 U/min·g, HY: 3.3856 U/min·g) in the HY group were significantly lower compared with the natural fermentation group (ZY), while acid lipase activity (ZY: 0.3184 U/h·g, HY: 0.7075 U/h·g) and neutral lipase activity (ZY: 12.65443 U/h·g, HY: 20.25142 U/h·g) were significantly higher than the control sample. Totally 40 differential fatty acid metabolites were screened. Arachidonic acid metabolism, unsaturated fatty acid biosynthesis and linoleic acid metabolism were potential metabolic pathways. Seven major bacterial species were closely associated with 15 differential fatty acid. This study contributes to the targeted production of fatty acid functional active substances of YJS.

Microbial interactions shape cheese flavour formation

Cheese fermentation and flavour formation are the result of complex biochemical reactions driven by the activity of multiple microorganisms. Here, we studied the roles of microbial interactions in flavour formation in a year-long Cheddar cheese making process, using a commercial starter culture containing Streptococcus thermophilus and Lactococcus strains. By using an experimental strategy whereby certain strains were left out from the starter culture, we show that S. thermophilus has a crucial role in boosting Lactococcus growth and shaping flavour compound profile. Controlled milk fermentations with systematic exclusion of single Lactococcus strains, combined with genomics, genome-scale metabolic modelling, and metatranscriptomics, indicated that S. thermophilus proteolytic activity relieves nitrogen limitation for Lactococcus and boosts de novo nucleotide biosynthesis. While S. thermophilus had large contribution to the flavour profile, Lactococcus cremoris also played a role by limiting diacetyl and acetoin formation, which otherwise results in an off-flavour when in excess. This off-flavour control could be attributed to the metabolic re-routing of citrate by L. cremoris from diacetyl and acetoin towards α-ketoglutarate. Further, closely related Lactococcus lactis strains exhibited different interaction patterns with S. thermophilus, highlighting the significance of strain specificity in cheese making. Our results highlight the crucial roles of competitive and cooperative microbial interactions in shaping cheese flavour profile.

Combined application of high-throughput sequencing and LC-MS-based lipidomics in the evaluation of microorganisms and lipidomics of restructured ham of different salted substitution

The optimization of processed meats through salt replacement using KCl and k-lactate may reduce the risk of chronic diseases through reduction in dietary sodium. The objective of this study was to investigate the changes and relationships between microbial and lipid metabolism during the fermentation of restructured duck ham with different salt substitutions. Lactobacillus and Staphylococcus were found to be the dominant bacterial species in the 30 % KCl + 70 % NaCl (w/w) and 25 % k-lactate + 75 % NaCl (w/w). The LefSe analysis showed that different biomarkers were present in different ham groups, and the PLS-DA showed that triglycerides (GL) and glycerophospholipids (GP) were the two classes with the highest abundance. Besides, the KEGG pathway analysis revealed that glycerophospholipid metabolism and triglyceride metabolism were also the main metabolic pathways. According to the correlation study, Staphylococcus, Halomonas, and Lactobacillus were mostly linked to the important metabolic pathways in restructured ham. Our findings serve as a foundation for quality assurance and product enhancement for low-salt restructured ham.

A bibliometric analysis of the global impact of metaproteomics research

Background

Metaproteomics is a subfield in meta-omics that is used to characterize the proteome of a microbial community. Despite its importance and the plethora of publications in different research area, scientists struggle to fully comprehend its functional impact on the study of microbiomes. In this study, bibliometric analyses are used to evaluate the current state of metaproteomic research globally as well as evaluate the specific contribution of Africa to this burgeoning research area. In this study, we use bibliometric analyses to evaluate the current state of metaproteomic research globally, identify research frontiers and hotspots, and further predict future trends in metaproteomics. The specific contribution of Africa to this research area was evaluated.

Methods

Relevant documents from 2004 to 2022 were extracted from the Scopus database. The documents were subjected to bibliometric analyses and visualization using VOS viewer and Biblioshiny package in R. Factors such as the trends in publication, country and institutional cooperation networks, leading scientific journals, author's productivity, and keywords analyses were conducted. The African publications were ranked using Field-Weighted Citation Impact (FWCI) scores.

Results

A total of 1,138 documents were included and the number of publications increased drastically from 2004 to 2022 with more publications (170) reported in 2021. In terms of publishers, Frontiers in Microbiology had the highest number of total publications (62). The United States of America (USA), Germany, China, and Canada, together with other European countries were the most productive. Institution-wise, the Helmholtz Zentrum für Umweltforschung, Germany had more publications while Max Plank Institute had the highest total collaborative link strength. Jehmlich N. was the most productive author whereas Hettich RL had the highest h-index of 63. Regarding Africa, only 2.2% of the overall publications were from the continent with more publication outputs from South Africa. More than half of the publications from the continent had an FWCI score ≥ 1.

Conclusion

The scientific outputs of metaproteomics are rapidly evolving with developed countries leading the way. Although Africa showed prospects for future progress, this could only be accelerated by providing funding, increased collaborations, and mentorship programs.

Quorum sensing-mediated microbial interactions: Mechanisms, applications, challenges and perspectives

Microbial community in natural or artificial environments playes critical roles in substance cycles, products synthesis and species evolution. Although microbial community structures have been revealed via culture-dependent and culture-independent approaches, the hidden forces driving the microbial community are rarely systematically discussed. As a mode of cell-to-cell communication that modifies microbial interactions, quorum sensing can regulate biofilm formation, public goods secretion, and antimicrobial substances synthesis, directly or indirectly influencing microbial community to adapt to the changing environment. Therefore, the current review focuses on microbial community in the different habitats from the quorum sensing perspective. Firstly, the definition and classification of quorum sensing were simply introduced. Subsequently, the relationships between quorum sensing and microbial interactions were deeply explored. The latest progressives regarding the applications of quorum sensing in wastewater treatment, human health, food fermentation, and synthetic biology were summarized in detail. Finally, the bottlenecks and outlooks of quorum sensing driving microbial community were adequately discussed. To our knowledge, this current review is the first to reveal the driving force of microbial community from the quorum sensing perspective. Hopefully, this review provides a theoretical basis for developing effective and convenient approaches to control the microbial community with quorum sensing approaches.

Causality Verification for the Correlation between the Presence of Nonstarter Bacteria and Flavor Characteristics in Soft-Type Ripened Cheeses

Flavor characteristics of ripened cheese are established by various bacteria, such as lactic acid bacteria, Actinobacteria, and Proteobacteria, which spontaneously develop during the cheese-manufacturing process. We previously revealed the relationship between bacterial microbiota and flavor components in soft-type ripened cheeses by using a multiomics approach that combined metagenomics and metabolomics; however, we could not establish a causal relationship. This study aimed to substantiate the causal nature of the correlations revealed by the multiomics approach by using cheese-ripening tests with single isolate inoculation. The bacterial diversity and composition in surface mold-ripened cheeses from Japan and France varied, depending on the differences between the milks (pasteurized or raw), cheese positions (core or rind), and manufacturers. Although the volatile compounds did not clearly reflect the distinctive characteristics of the cheese samples, nonstarter lactic acid bacteria, Actinobacteria, and Proteobacteria positively correlated with ketones and sulfur compounds, as evidenced by a Spearman's correlation analysis. Cheese-ripening tests conducted after inoculation with single bacterial strains belonging to the above-mentioned taxa confirmed that these bacteria formed volatile compounds, in agreement with the correlations observed. In particular, various flavor compounds, such as acids, esters, ketones, and sulfur compounds, were detected in cheese inoculated with Pseudoalteromonas sp. TS-4-4 strain. These findings provide important insights into the role of nonstarter bacteria in the development of cheese flavor and into the effectiveness of the multiomics approach in screening for bacteria that can improve the quality of cheese products. IMPORTANCE Our previous study revealed that the existence of various bacteria, such as lactic acid bacteria, Actinobacteria, and Proteobacteria, clearly correlated with the abundance of flavor components, such as volatile compounds, in soft-type ripened cheeses via a multiomics approach that used 16S rRNA gene amplicon sequencing and headspace gas chromatography-mass spectrometry. However, this approach only showed correlations derived from statistical analyses rather than causal relationships. Therefore, in the present study, we performed cheese-ripening tests using nonstarter bacteria to substantiate the correlations revealed by the multiomics approach in soft-type ripened cheese. Our results suggest the capability of nonstarter bacteria, such as Proteobacteria, to impart flavor to cheese and the effectiveness of the multiomics approach in screening for microbial isolates that can improve the quality of cheese. Overall, our research provides new insights into the importance of bacteria in cheese production.

The Application of Metagenomics to Study Microbial Communities and Develop Desirable Traits in Fermented Foods

The microbial communities present within fermented foods are diverse and dynamic, producing a variety of metabolites responsible for the fermentation processes, imparting characteristic organoleptic qualities and health-promoting traits, and maintaining microbiological safety of fermented foods. In this context, it is crucial to study these microbial communities to characterise fermented foods and the production processes involved. High Throughput Sequencing (HTS)-based methods such as metagenomics enable microbial community studies through amplicon and shotgun sequencing approaches. As the field constantly develops, sequencing technologies are becoming more accessible, affordable and accurate with a further shift from short read to long read sequencing being observed. Metagenomics is enjoying wide-spread application in fermented food studies and in recent years is also being employed in concert with synthetic biology techniques to help tackle problems with the large amounts of waste generated in the food sector. This review presents an introduction to current sequencing technologies and the benefits of their application in fermented foods.