Structure of association networks in food bacterial communities

Integration of metataxonomic data sets into microbial association networks highlights shared bacterial community dynamics in fermented vegetables

The management of food fermentation is still largely based on empirical knowledge, as the dynamics of microbial communities and the underlying metabolic networks that produce safe and nutritious products remain beyond our understanding. Although these closed ecosystems contain relatively few taxa, they have not yet been thoroughly characterized with respect to how their microbial communities interact and dynamically evolve. However, with the increased availability of metataxonomic data sets on different fermented vegetables, it is now possible to gain a comprehensive understanding of the microbial relationships that structure plant fermentation. In this study, we applied a network-based approach to the integration of public metataxonomic 16S data sets targeting different fermented vegetables throughout time. Specifically, we aimed to explore, compare, and combine public 16S data sets to identify shared associations between amplicon sequence variants (ASVs) obtained from independent studies. The workflow includes steps for searching and selecting public time-series data sets and constructing association networks of ASVs based on co-abundance metrics. Networks for individual data sets are then integrated into a core network, highlighting significant associations. Microbial communities are identified based on the comparison and clustering of ASV networks using the "stochastic block model" method. When we applied this method to 10 public data sets (including a total of 931 samples) targeting five varieties of vegetables with different sampling times, we found that it was able to shed light on the dynamics of vegetable fermentation by characterizing the processes of community succession among different bacterial assemblages.

IMPORTANCE

Within the growing body of research on the bacterial communities involved in the fermentation of vegetables, there is particular interest in discovering the species or consortia that drive different fermentation steps. This integrative analysis demonstrates that the reuse and integration of public microbiome data sets can provide new insights into a little-known biotope. Our most important finding is the recurrent but transient appearance, at the beginning of vegetable fermentation, of amplicon sequence variants (ASVs) belonging to Enterobacterales and their associations with ASVs belonging to Lactobacillales. These findings could be applied to the design of new fermented products.

Utilizing co-abundances of antimicrobial resistance genes to identify potential co-selection in the resistome

The rapid spread of antimicrobial resistance (AMR) is a threat to global health, and the nature of co-occurring antimicrobial resistance genes (ARGs) may cause collateral AMR effects once antimicrobial agents are used. Therefore, it is essential to identify which pairs of ARGs co-occur. Given the wealth of next-generation sequencing data available in public repositories, we have investigated the correlation between ARG abundances in a collection of 214,095 metagenomic data sets. Using more than 6.76∙108 read fragments aligned to acquired ARGs to infer pairwise correlation coefficients, we found that more ARGs correlated with each other in human and animal sampling origins than in soil and water environments. Furthermore, we argued that the correlations could serve as risk profiles of resistance co-occurring to critically important antimicrobials (CIAs). Using these profiles, we found evidence of several ARGs conferring resistance for CIAs being co-abundant, such as tetracycline ARGs correlating with most other forms of resistance. In conclusion, this study highlights the important ARG players indirectly involved in shaping the resistomes of various environments that can serve as monitoring targets in AMR surveillance programs.

IMPORTANCE

Understanding the collateral effects happening in a resistome can reveal previously unknown links between antimicrobial resistance genes (ARGs). Through the analysis of pairwise ARG abundances in 214K metagenomic samples, we observed that the co-abundance is highly dependent on the environmental context and argue that these correlations can be used to show the risk of co-selection occurring in different settings.

A Comprehensive View of Food Microbiota: Introducing FoodMicrobionet v5

Amplicon-targeted metagenomics is now the standard approach for the study of the composition and dynamics of food microbial communities. Hundreds of papers on this subject have been published in scientific journals and the information is dispersed in a variety of sources, while raw sequences and their metadata are available in public repositories for some, but not all, of the published studies. A limited number of web resources and databases allow scientists to access this wealth of information but their level of annotation on studies and samples varies. Here, we report on the release of FoodMicrobionet v5, a comprehensive database of metataxonomic studies on bacterial and fungal communities of foods. The current version of the database includes 251 published studies (11 focusing on fungal microbiota, 230 on bacterial microbiota, and 10 providing data for both bacterial and fungal microbiota) and 14,035 samples with data on bacteria and 1114 samples with data on fungi. The new structure of the database is compatible with interactive apps and scripts developed for previous versions and allows scientists, R&D personnel in industries and regulators to access a wealth of information on food microbial communities.

Microbiome dynamics, antibiotic resistance gene patterns and spoilage-associated genomic potential in fresh anchovies stored in different conditions

Fresh fish is a highly perishable product and is easily spoiled by microbiological activity and chemical oxidation of lipids. However, microbial spoilage is the main factor linked with the rapid fish sensorial degradation due to the action of specific spoilage organisms (SSOs) that have the ability to dominate over other microorganisms and produce metabolites responsible for off-flavours. We explored the microbial dynamics in fresh anchovies stored in different packaging (air, modified atmosphere, under vacuum) and temperatures (0, 4 and 10 °C) using shotgun metagenomics, highlighting the selection of different microbial species according to the packaging type. Indeed, Pseudoalteromonas nigrifaciens, Psychrobacter cryohalolentis and Ps. immobilis, Pseudomonas deceptionensis and Vibrio splendidus have been identified as the main SSOs in aerobically stored anchovies, while Shewanella baltica, Photobacterium iliopiscarium, Ps. cryohalolentis and Ps. immobilis prevailed in VP and MAP. In addition, we identified the presence of spoilage-associated genes, leading to the potential production of biogenic amines and different off-flavors (H2S, TMA). In particular, the abundance of microbial genes leading to BA biosynthesis increased at higher storage temperature, while those related to H2S and TMA production were enriched in aerobically and VP packed anchovies, suggesting that MAP could be an effective strategy in delaying the production of these compounds. Finally, we provided evidence of the presence of a wide range of antibiotic resistance genes conferring resistance to different classes of antibiotic (β-lactams, tetracyclines, polymyxins, trimethoprims and phenicols) and highlighted that storage at higher temperature (4 and 10 °C) boosted the abundance of ARG-carrying taxa, especially in aerobically and MAP packed fish.

Dynamic Changes of Bacterial Communities and Microbial Association Networks in Ready-to-Eat Chicken Meat during Storage

Ready-to-eat (RTE) chicken is a popular food in China, but its lack of food safety due to bacterial contamination remains a concern, and the dynamic changes of microbial association networks during storage are not fully understood. This study investigated the impact of storage time and temperature on bacterial compositions and microbial association networks in RTE chicken using 16S rDNA high-throughput sequencing. The results show that the predominant phyla present in all samples were Proteobacteria and Firmicutes, and the most abundant genera were Weissella, Pseudomonas and Proteus. Increased storage time and temperature decreased the richness and diversity of the microorganisms of the bacterial communities. Higher storage temperatures impacted the bacterial community composition more significantly. Microbial interaction analyses showed 22 positive and 6 negative interactions at 4 °C, 30 positive and 12 negative interactions at 8 °C and 44 positive and 45 negative interactions at 22 °C, indicating an increase in the complexity of interaction networks with an increase in the storage temperature. Enterobacter dominated the interactions during storage at 4 and 22 °C, and Pseudomonas did so at 22 °C. Moreover, interactions between pathogenic and/or spoilage bacteria, such as those between Pseudomonas fragi and Weissella viridescens, Enterobacter unclassified and Proteus unclassified, or those between Enterobacteriaceae unclassified and W.viridescens, were observed. This study provides insight into the process involved in RTE meat spoilage and can aid in improving the quality and safety of RTE meat products to reduce outbreaks of foodborne illness.

Study of Wetland Soils of the Salar de Atacama with Different Azonal Vegetative Formations Reveals Changes in the Microbiota Associated with Hygrophile Plant Type on the Soil Surface

Salar de Atacama is located approximately 55 km south of San Pedro de Atacama in the Antofagasta region, Chile. The high UV irradiation and salt concentration and extreme drought make Salar de Atacama an ideal site to search for novel soil microorganisms with unique properties. Here, we used a metataxonomic approach (16S rRNA V3-V4) to identify and characterize the soil microbiota associated with different surface azonal vegetation formations, including strict hygrophiles (Baccharis juncea, Juncus balticus, and Schoenoplectus americanus), transitional hygrophiles (Distichlis spicata, Lycium humile, and Tessaria absinthioides), and their various combinations. We detected compositional differences among the soil surface microbiota associated with each plant formation in the sampling area. There were changes in soil microbial phylogenetic diversity from the strict to the transitional hygrophiles. Moreover, we found alterations in the abundance of bacterial phyla and genera. Halobacteriota and Actinobacteriota might have facilitated water uptake by the transitional hygrophiles. Our findings helped to elucidate the microbiota of Salar de Atacama and associate them with the strict and transitional hygrophiles indigenous to the region. These findings could be highly relevant to future research on the symbiotic relationships between microbiota and salt-tolerant plants in the face of climate change-induced desertification. IMPORTANCE The study of the composition and diversity of the wetland soil microbiota associated with hygrophilous plants in a desert ecosystem of the high Puna in northern Chile makes it an ideal approach to search for novel extremophilic microorganisms with unique properties. These microorganisms are adapted to survive in ecological niches, such as those with high UV irradiation, extreme drought, and high salt concentration; they can be applied in various fields, such as biotechnology and astrobiology, and industries, including the pharmaceutical, food, agricultural, biofuel, cosmetic, and textile industries. These microorganisms can also be used for ecological conservation and restoration. Extreme ecosystems are a unique biological resource and biodiversity hot spots that play a crucial role in maintaining environmental sustainability. The findings could be highly relevant to future research on the symbiotic relationships between microbiota and extreme-environment-tolerant plants in the face of climate change-induced desertification.

Characterization of bacterial communities in Coregonus peled fillets during chilled storage and interactions between selected bacterial strains

AIM

Coregonus peled fillets were used as a model to evaluate the dominant bacterial growth of chilled fish during storage after shipping and interactions of selected bacterial strains.

METHODS AND RESULTS

C. peled fillets were transported by air and land in ice boxes about 48 h from aquatic products company in Xinjiang, China to the laboratory located in Dalian, China. Both culture-dependent methods (plate counts on nonselective media) based on 16S rRNA gene sequencing and culture-independent methods (Illumina-MiSeq high-throughput sequencing) were used. To detect interactions among bacterial populations from chilled fish, the influence of 18 test strains on the growth of 12 indicator isolates was measured by a drop assay and in liquid culture medium broth. The results showed that bacterial counts exceeded 7.0 log CFU/g following 4 days storage at 4 °C. When the bacterial counts exceeded 8.5 log CFU/g after 12 days, the predominant microorganisms were Aeromonas, Pseudomonas, Carnobacterium, Psychrobacter and Shewanella, as measured by culture-independent methods. All test strains showed inhibiting effects on the growth of other strains in liquid culture. Pseudomonas isolates showed antibacterial activity for approximately 60% of the indicator strains on nutritional agar plates. The majority of test isolates enhancing indicator strain growth were the strains isolated on day 0.

CONCLUSIONS

High-throughput sequencing approach gives whole picture of bacterial communities in C.peled fillets during storage, while growth interferences between selected bacterial strains illustrate the complexity of microbial interactions.

SIGNIFICANCE AND IMPACT OF THE STUDY

We determined the bacterial communities and growth interferences in chilled C.peled after shipping and these are the first data concerning microbiota in C.peled using a culture-independent analysis. The present study will be useful for manufacture and preservation of C.peled products by providing with valuable information regarding microbiological spoilage of C.peled.

The interaction of acidophiles driving community functional responses to the re-inoculated chalcopyrite bioleaching process

Re-inoculation was an effective way to improve bioleaching efficiency by enhancing the synergetic effects of biogenic Fe³⁺ coupling with S⁰ oxidation. However, the complex microbial interactions after re-inoculation have received far less attention, which was crucial to the bioleaching performances. Herein, the enriched ferrous oxidizers (FeO) or sulfur oxidizers (SO) were inoculated to chalcopyrite microcosm, then they were crossly re-inoculated again to characterize the interspecific interaction patterns. The results showed that the dominant species in Fe groups were Acidithiobacillus ferrooxidans, while A. thiooxidans predominated in S groups. Introducing FeO resulted in a great disturbance by shifting the community diversity and evenness significantly (p < 0.05). In comparison, the communities intensified by SO maintained the original composition and structures. Microbial networks were constructed positively and modularly. The networks intensified by FeO were less connected and complex with less nodes and edges, but showed faster responses to the re-inoculation disturbance reflected by shorter average path length. Interestingly, the genus Leptospirillum were identified as keystones in S groups, playing critical roles in iron-oxidizing with lots of sulfur oxidizers. The introduced sulfur oxidizers enhanced microbial cooperation, formed robust community with strong bio-dissolution capability, and harbored the highest bioleaching efficiency. These findings improved our understanding about the acidophiles interactions, which drive community functional responses to the re-inoculated bioleaching process.

Mono-specific algal diets shape microbial networking in the gut of the sea urchin Tripneustes gratilla elatensis

BACKGROUND

Algivorous sea urchins can obtain energy from a diet of a single algal species, which may result in consequent changes in their gut microbe assemblies and association networks.

METHODS

To ascertain whether such changes are led by specific microbes or limited to a specific region in the gut, we compared the microbial assembly in the three major gut regions of the sea urchin Tripneustes gratilla elatensis when fed a mono-specific algal diet of either Ulva fasciata or Gracilaria conferta, or an algal-free diet. DNA extracts from 5 to 7 individuals from each diet treatment were used for Illumina MiSeq based 16S rRNA gene sequencing (V3-V4 region). Niche breadth of each microbe in the assembly was calculated for identification of core, generalist, specialist, or unique microbes. Network analyzers were used to measure the connectivity of the entire assembly and of each of the microbes within it and whether it altered with a given diet or gut region. Lastly, the predicted metabolic functions of key microbes in the gut were analyzed to evaluate their potential contribution to decomposition of dietary algal polysaccharides.

RESULTS

Sea urchins fed with U. fasciata grew faster and their gut microbiome network was rich in bacterial associations (edges) and networking clusters. Bacteroidetes was the keystone microbe phylum in the gut, with core, generalist, and specialist representatives. A few microbes of this phylum were central hub nodes that maintained community connectivity, while others were driver microbes that led the rewiring of the assembly network based on diet type through changes in their associations and centrality. Niche breadth agreed with microbes' richness in genes for carbohydrate active enzymes and correlated Bacteroidetes specialists to decomposition of specific polysaccharides in the algal diets.

CONCLUSIONS

The dense and well-connected microbial network in the gut of Ulva-fed sea urchins, together with animal's rapid growth, may suggest that this alga was most nutritious among the experimental diets. Our findings expand the knowledge on the gut microbial assembly in T. gratilla elatensis and strengthen the correlation between microbes' generalism or specialism in terms of occurrence in different niches and their metabolic arsenal which may aid host nutrition.

Metagenomic Analysis of Bacterial Diversity in Traditional Fermented Foods Reveals Food-Specific Dominance of Specific Bacterial Taxa

Traditional fermented foods have been recognized by various communities to be good for health since ancient times. There is a provincial legacy of traditional fermented foods among the ethnic population of North-East India. Fermented bamboo shoots (local name: Tuaither), soybeans (Bekang), and pork fat (Sa-um) are famous in the Mizoram state and represent a primary portion of the daily diet. These foods are prepared using methods based on cultural traditions inherited from previous generations, and prepared using a relatively uncontrolled fermentation process. Analysis of the bacterial diversity in these foods can provide important information regarding the flavor and texture of the final products of fermentation. Unfortunately, studies on the microbial composition and health benefits of such traditional fermented foods have rarely been documented. Therefore, the present study aims to highlight this bacterial diversity, along with the proximate composition of different traditional fermented foods (Tuaither, Bekang and Sa-um) primarily consumed in Mizoram state, India. Samples were collected on three different days of fermentation (3rd, 5th and 7th day), and bacterial diversity analysis was performed using the V3-V4 variable region of 16S rRNA gene with Illumina sequencing. Results revealed differences in the bacterial composition of dominant group members among all of the three food types. Firmicutes (82.72–94.00%), followed by Proteobacteria (4.67–15.01%), were found to dominate to varying degrees in all three of the fermented foods. However, at genus level high variation was observed in bacterial composition among these three different types of fermented foods. Lactobacillus (91.64–77.16%), Staphylococcus (52.00–17.90%), and Clostridium (72.48–55.40%) exhibited the highest relative abundances in the Tuaither, Bekang and Sa-um foods, respectively, in descending order from the 3rd to 7th day of fermentation. A few of the bacterial genera such as Lactobacilli were positively correlated with fermented bamboo shoot samples, and Staphylococcus was positively correlated with protein, carbohydrate and crude fiber content in soybean samples. In general, Tuaither, Bekang and Sa-um exhibited distinct differences in bacterial composition. This variation may be due to differences in the raw materials and/or methods used in the preparation of the different fermented food products. This is the first study to describe the bacterial composition of these traditional fermented foods using high-throughput sequencing techniques, and could help to drive research attention to comprehensive studies on improving understanding of the role of microbial communities in the preparation of traditional foods and their health benefits.

Fermented food products in the era of globalization: tradition meets biotechnology innovations

Omics tools offer the opportunity to characterize and trace traditional and industrial fermented foods. Bioinformatics, through machine learning, and other advanced statistical approaches, are able to disentangle fermentation processes and to predict the evolution and metabolic outcomes of a food microbial ecosystem. By assembling microbial artificial consortia, the biotechnological advances will also be able to enhance the nutritional value and organoleptics characteristics of fermented food, preserving, at the same time, the potential of autochthonous microbial consortia and metabolic pathways, which are difficult to reproduce. Preserving the traditional methods contributes to protecting the hidden value of local biodiversity, and exploits its potential in industrial processes with the final aim of guaranteeing food security and safety, even in developing countries.

A continuously changing selective context on microbial communities associated with fish, from egg to fork

Fast increase of fish aquaculture production to meet consumer demands is accompanied by important ecological concerns such as disease outbreaks. Meanwhile, food waste is an important concern with fish products since they are highly perishable. Recent aquaculture and fish product microbiology, and more recently, microbiota research, paved the way to a highly integrated approach to understand complex relationships between host fish, product and their associated microbial communities at health/disease and preservation/spoilage frontiers. Microbial manipulation strategies are increasingly validated as promising tools either to replace or to complement traditional veterinary and preservation methods. In this review, we consider evolutionary forces driving fish microbiota assembly, in particular the changes in the selective context along the production chain. We summarize the current knowledge concerning factors governing assembly and dynamics of fish hosts and food microbial communities. Then, we discuss the current microbial community manipulation strategies from an evolutionary standpoint to provide a perspective on the potential for risks, conflict and opportunities. Finally, we conclude that to harness evolutionary forces in the development of sustainable microbiota manipulation applications in the fish industry, an integrated knowledge of the controlling abiotic and especially biotic factors is required.

Integrative study of the upper and lower airway microbiome and transcriptome in asthma

Relatively little is known about interactions between the airway microbiome and airway host transcriptome in asthma. Since asthma affects and is affected by the entire airway, studying the upper (e.g., nasal) and lower (e.g., bronchial) airways together represents a powerful approach to understanding asthma. Here, we performed a systematic, integrative study of the nasal and bronchial microbiomes and nasal and bronchial host transcriptomes of children with severe persistent asthma and healthy controls. We found that (a) the microbiomes and host transcriptomes of asthmatic children are each distinct by site (nasal versus bronchial); (b) among asthmatic children, Moraxella and Alloiococcus are hub genera in the nasal microbiome, while there are no hubs among bronchial genera; (c) bronchial Actinomyces is negatively associated with bronchial genes for inflammation, suggesting Actinomyces may be protective; (d) compared with healthy children, asthmatic children express more nasal genes for ciliary function and harbor more nasal Streptococcus; and (e) nasal genera such as Corynebacterium are negatively associated with significantly more nasal genes for inflammation in healthy versus asthmatic children, suggesting a potentially stronger protective role for such nasal genera in healthy versus asthmatic children. Our systematic, integrative study provides a window into host-microbiome associations in asthma.

Tracking bacteriome variation over time in Listeria monocytogenes-positive foci in food industry

The variation in microbial composition over time was assessed in biofilms formed in situ on selected non-food and food contact surfaces of meat and fish industries, previously identified as Listeria monocytogenes-positive foci. First, all samples were analysed for the detection and quantification of L. monocytogenes using ISO 11290-1 and ISO 11290-2 norms, respectively. Although the pathogen was initially detected in all samples, direct quantification was not possible. Psychrotrophic bacteria counts were among resident microbiota in meat industry samples (Mean_max = 6.14 log CFU/cm²) compared to those form fish industry (Mean_max = 5.85 log CFU/cm²). Visual analysis of the biofilms using epifluorescence microscopy revealed a trend to form microcolonies in which damaged/dead cells would act as anchoring structures. 16S rRNA gene metagenetic analysis demonstrated that, although Proteobacteria (71.37%) initially dominated the bacterial communities at one meat industry location, there was a dramatic shift in composition as the biofilms matured, where Actinobacteria (79.72%) became the major phylum present in later samples. This change was largely due to an increase of Nocardiaceae, Micrococcaceae and Microbacteriaceae. Nevertheless, for the other sampling location, the relative abundance of the dominating phylum (Firmicutes) remained consistent over the entire sampling period (Mean = 63.02%). In fish industry samples, Proteobacteria also initially dominated early on (90.69%) but subsequent sampling showed a higher diversity in which Bacteroidetes and Proteobacteria were the most abundant phyla accounting for the 48.04 and 37.98%, respectively by the last sampling period. Regardless of the location, the community profiles of the endpoint samples were similar to those reported previously. This demonstrated that in a given industrial setting there is a trend to establish a determinate biofilm structure due to the environmental factors and the constant incoming microbiota. This information could be used to improve the existing sanitisation protocols or for the design of novel strategies.

Physiological traits and relative abundance of species as explanatory variables of co-occurrence pattern of cultivable bacteria associated with chia seeds

Deciphering the rules defining microbial community assemblage is envisioned as a promising strategy to improve predictions of pathogens colonization and proliferation in food. Despite the increasing number of studies reporting microbial co-occurrence patterns, only a few attempts have been made to challenge them in experimental or theoretical frameworks. Here, we tested the hypothesis that observed variations in co-occurrence patterns can be explained by taxonomy, relative abundance, and physiological traits of microbial species. We used PCR amplicon sequencing of taxonomic markers to assess distribution and co-occurrence patterns of bacterial and fungal species found in 25 chia (Salvia hispanica L.) samples originating from eight different sources. The use of nutrient-rich and oligotrophic media enabled isolation of 71 strains encompassing 16 bacterial species, of which five corresponded to phylotypes represented in the molecular survey. Tolerance to different growth inhibitors and antibiotics was tested to assess the physiological traits of these isolates. Divergence of physiological traits and relative abundance of each pair of species explained 69% of the co-occurrence profile displayed by cultivable bacterial phylotypes in chia. Validation of this ecological network conceptualization approach to more food products is required to integrate microbial species co-occurrence patterns in predictive microbiology.