Characterization of microbial community structure and metabolic potential using Illumina MiSeq platform during the black garlic processing

Structure-anti-inflammatory activity relationship of garlic fructans in mice with dextran sulfate sodium-induced colitis: Impact of chain length

The present study identified the protective effects of garlic oligo/poly-saccharides of different chain lengths against dextran sulfate sodium (DSS)-induced colitis in mice and elucidated the structure-function relationships. The results showed that oral intake of garlic oligo/poly-saccharides decreased disease activity index, reduced colon shortening and spleen enlargement, and ameliorated pathological damage in the mouse colon. The dysregulation of colonic pro/anti-inflammatory cytokines was significantly alleviated, accompanied by up-regulated antioxidant enzymes, blocked TLR4-MyD88-NF-κB signaling pathway, enhanced intestinal barrier integrity, and restored SCFA production. Garlic oligo/poly-saccharides also reversed gut microbiota dysbiosis in colitic mice by expanding beneficial bacteria and suppressing the growth of harmful bacteria. High-molecular-weight polysaccharides exhibited stronger alleviating effects on DSS-induced colitic symptoms in mice than low-molecular-weight oligo/poly-saccharides did, probably due to their greater ability to be fermented in the colon. Taken together, this study demonstrated the anti-inflammatory effects of garlic oligo/poly-saccharides and revealed that high-molecular-weight polysaccharide fractions were more effective in alleviating DSS-induced colitis.

Psychochemical changes and functional properties of organosulfur and polysaccharide compounds of black garlic (Allium sativum L.)

Background

Black garlic is one of the functional food products made from garlic which is processed through aging to improve sensory value and nutritional quality. Aging conditions has a major impact on the psychochemical and functional properties changes of black garlic which is closely related to organosulfur compounds and polysaccharides as the largest component in garlic.

Scope and approach

The method used in this research is a systematic review with the aim of research to determine the relationship between reactions during aging and changes in organosulfur, polysaccharides and non-enzymatic browning product compounds as well as the function of black garlic by focusing on certain aspects of aging including temperature, humidity, time, microorganism activity, and pre-treatment application.

Key findings and conclusions

Maillard reaction and polysaccharide degradation are still be the dominant reactions and play an important role in black garlic production. High hydrostatic pressure pretreatment could maintains the quality of black garlic so that the black garlic has the same taste characteristics as black garlic in general. Antioxidant properties in black garlic shown increase during thermal treatment. In addition, it is known that the activity of microorganisms plays a role and being potential to increase the quality value of black garlic as well as the antimicrobial activity.

Impact of artisanal refining activities on bacterial diversity in a Niger Delta fallow land

Hydrocarbon pollution is a major ecological problem facing oil-producing countries, especially in the Niger Delta region of Nigeria. In this study, a site that had been previously polluted by artisanal refining activity was investigated using 16S rRNA Illumina high-throughput sequencing technology and bioinformatics tools. These were used to investigate the bacterial diversity in soil with varying degrees of contamination, determined with a gas chromatography-flame ionization detector (GC-FID). Soil samples were collected from a heavily polluted (HP), mildly polluted (MP), and unpolluted (control sample, CS) portion of the study site. DNA was extracted using the Zymo Research (ZR) Fungi/Bacteria DNA MiniPrep kit, followed by PCR amplification and agarose gel electrophoresis. The microbiome was characterized based on the V3 and V4 hypervariable regions of the 16S rRNA gene. QIIME (Quantitative Insights Into Microbial Ecology) 2 software was used to analyse the sequence data. The final data set covered 20,640 demultiplexed high-quality reads and a total of 160 filtered bacterial OTUs. Proteobacteria dominated samples HP and CS, while Actinobacteria dominated sample MP. Denitratisoma, Pseudorhodoplanes, and Spirilospora were the leading genera in samples HP, CS, and MP respectively. Diversity analysis indicated that CS [with 25.98 ppm of total petroleum hydrocarbon (TPH)] is more diverse than HP (with 490,630 ppm of TPH) and MP (with 5398 ppm of TPH). A functional prediction study revealed that six functional modules dominated the dataset, with metabolism covering up to 70%, and 11 metabolic pathways. This study demonstrates that a higher hydrocarbon concentration in soil adversely impacts microbial diversity, creating a narrow bacterial diversity dominated by hydrocarbon-degrading species, in addition to the obvious land and ecosystem degradation caused by artisanal refining activities. Overall, the artisanal refining business is significantly driving ecosystem services losses in the Niger Delta, which calls for urgent intervention, with focus on bioremediation.

Polyamine-producing bacteria inhibit the absorption of Cd by spinach and alter the bacterial community composition of rhizosphere soil

Polyamines (PAs) are small aliphatic nitrogenous bases with strong biological activity that participate in plant stress response signaling and the alleviation of damage from stress. Herein, the effects of the PA-producing bacterium Bacillus megaterium N3 and PAs on the immobilization of Cd and inhibition of Cd absorption by spinach and the underlying mechanisms were studied. A solution test showed that strain N3 secreted spermine and spermidine in the presence of Cd. Both strain N3 and the PAs (spermine+spermidine) immobilized Cd and increased the pH of the solution. Untargeted metabolomics results showed that strain N3 secreted PAs, N1-acetylspermidine, 3-indolepropionic acid, indole-3-acetaldehyde, cysteinyl-gamma-glutamate, and choline, which correlated with plant growth promotion and Cd immobilization. A pot experiment showed that rhizosphere soil inoculation with strain N3 and PAs improved spinach dry weight and reduced spinach Cd absorption compared with the control. These positive effects were likely due to the increase in rhizosphere soil pH and NH4+-N and PA contents, which can be attributed primarily to Cd immobilization. Moreover, inoculation with strain N3 more effectively inhibited the absorption of Cd by spinach than spraying PAs, mainly because strain N3 enabled a better relative abundance of bacteria (Microvirga, Pedobacter, Bacillus, Brevundimonas, Pseudomonas, Serratia, Devosid, and Aminobacter), that have been reported to have the ability to resist heavy metals and produce PAs. Strain N3 regulated the structure of rhizosphere functional bacterial communities and inhibited Cd uptake by spinach. These results provide a theoretical basis for the prevention of heavy metal absorption by vegetables using PA-producing bacteria.

Community Synergy of Lactic Acid Bacteria and Cleaner Fermentation of Oat Silage Prepared with a Multispecies Microbial Inoculant

To investigate community synergy of lactic acid bacteria (LAB) and cleaner fermentation of oat silage, oat silages were prepared with or without (control) commercial LAB inoculants LI1 (containing Lactiplantibacillus plantarum, Lentilactobacillus buchneri, Lacticaseibacillus paracasei, and Pediococcus acidilactici) and LI2 (containing Lactiplantibacillus plantarum and Lentilactobacillus buchneri). The microbial community, LAB synergy, and cleaner fermentation were analyzed at 1, 3, 6, 15, 35, and 90 days of ensiling. The LAB inoculant improved fermentation quality, with significantly (P < 0.05) lower pH, ammonia nitrogen content, and gas production and higher lactic acid and acetic acid contents than those of the control. Enterobacteriaceae was the main bacterial community in early stage of fermentation, which utilizes sugar to produce CO2 gas, causing dry matter (DM) and energy loss. As fermentation progressed, the microbial diversity decreased, and the microbial community shifted from Gram-negative to Gram-positive bacteria. The inoculation of multispecies LAB displayed community synergy; Pediococcus acidilactici formed a dominant community in the early stage of fermentation, which produced an acid and anaerobic environment for the subsequent growth of Lentilactobacillus and Lacticaseibacillus species, thus forming a LAB-dominated microbial community. The predicted functional profile indicated that the silage inoculated with LI1 enhanced the carbohydrate metabolism pathway but inhibited the amino acid metabolism pathway, which played a role in promoting faster lactic acid production, reducing the decomposition of protein to ammonia nitrogen, and improving the fermentation quality of silage. Therefore, oat silage can be processed to high-quality and cleaner fermented feed by using an LAB inoculant, and LI1 showed better efficiency than LI2. IMPORTANCE Oat natural silage is rich in Enterobacteriaceae, increasing gas production and fermentation loss. Lactic acid bacteria interact synergistically to form a dominant community during ensiling. Pediococci grow vigorously in the early stage of fermentation and create an anaerobic environment. Lactobacilli inhibit the harmful microorganisms and result in cleaner fermentation of oat silage.

Chimonanthus salicifolius extract alleviates DSS-induced colitis and regulates gut microbiota in mice

Ulcerative colitis is a chronic and recurrent gastrointestinal intestinal disease accompanied by inflammatory disorders, immunologic inadequacy, and intestinal flora dysbiosis, and current therapeutic pharmaceuticals have limited side effects. In this study, we revealed the extraction method of Chimonanthus salicifolius, analyzed the main component, compared the effect of its extract, Lactobacillus, and conventional drugs with different properties on DSS (dextran sodium sulfate)-induced colitis, and indicated extract regulatory properties of inestinal flora. A colitis model was established on experimental design, and BALB/c mice (male, 7 weeks old) were randomly assigned to five groups (n = 10): control, DSS model, Chimonanthus salicifolius extract (CSE), Lactobacillus rhamnosus GG (LGG), and 5-aminosalicylic acid (5-ASA) groups. The three treatments could alleviate the symptoms and remit inflammation induced by DSS, in which CSE and LGG groups could both decrease the proinflammatory cytokine IL-6, IL-8, and TNF-α levels and increase anti-inflammatory cytokines IL-10 and TGF-β. The CSE intervention significantly promoted the higher production of butyric acid than LGG and 5-ASA groups (p < .05) after DSS challenge. Analysis of intestinal flora showed that CSE administration remarkably decreased the relative abundance of pathogenic bacteria Heliobacteriaceae and Peptococcaceae and exhibited higher abundance of Lactobacillaceae and Bifidobacterium than LGG in intestinal tract of mice (p < .05). These findings indicated that Chimonanthus salicifolius extract may have been beneficial for preventing and treating colitis.

Multiomics provides insights into the succession of microbiota and metabolite during plant leaf fermentation

The quality of fermented plant products is closely related to microbial metabolism. Here, the associations of bacterial communities, metabolites, and functional genes were explored using multi-omics techniques based on plant leaf fermentation systems. The results showed significant changes in the structure of the microbial community, with a significant decrease in Firmicutes and a significant increase in Proteobacteria. In addition, the concentration of metabolites with antibacterial, antioxidant and aroma properties increased significantly, enhancing the quality of the fermented plant leaves. Integrated macrogenomic and metabolomic analyses indicated that amino acid metabolism could be key metabolic pathway affecting fermentation quality. Actinobacteria, Proteobacteria, Firmicutes were actively involved in tyrosine metabolism (ko00350) and phenylalanine metabolism (ko00360), and are presumed to be the major groups responsible for synthesizing growth and flavor compounds. This study emphasized the important role of microorganisms in the changes of metabolites during the fermentation of plant leaves.

Analysis of Microbial Diversity and Metabolites in Sauerkraut Products with and without Microorganism Addition

The microbial compositions and metabolites of fermented sauerkraut with and without the addition of microorganisms have been compared. The OTU clustering, nonvolatile compounds, volatile compounds and associations between bacterial taxa and metabolites were analyzed by 16S rRNA high-throughput sequencing technology, ultra performance liquid chromatography (UPLC), gas chromatography ion mobility mass spectrometry (GC-IMS) and the O2PLS model studies. The results showed that at the phylum level, the microbial species in the four sauerkraut types consisted mainly of the phyla Firmicutes and Proteobacteria, but different modes of microbial addition formed their own unique microbial communities. There were significant differences in the microbial communities among different northeast China sauerkraut samples, and different microbial communities exerted similar effects to inhibit Firmicutes production. At the genus level, sauerkraut without added microorganisms had the lowest microbial diversity. A total of 26 amino acids and 11 organic acids were identified and were more abundant in nonmicrobially fermented sauerkraut; 88 volatile organic compounds were identified in the 4 types of sauerkraut, with the microbially fermented sauerkraut being richer in alcohols, esters and acids. Different brands of sauerkraut contain their own unique flavor compounds. Cystine and tyrosine, ascorbic acid and acetic acid, and alcohols and esters are closely related to a wide range of microorganisms in sauerkraut. Elucidating the correlations among microbiota and metabolites will help guide future improvements in sauerkraut fermentation processes.

Effects of different additives on the bacterial community and fermentation mode of whole-plant paper mulberry silage

The purpose of this study was to investigate the effects of inoculation with two lactic acid bacteria (LAB) strains (Lacticaseibacillus rhamnosus and Lentilactobacillus buchneri) and the addition of four corn flour proportions (0, 3, 6, and 9%) in different treatments, on the composition and function of the bacterial community in whole-plant paper mulberry silage. The different treatments promoted Lactiplantibacillus, Lentilactobacillus, and Lacticaseibacillus growth, but the microbial species responsible for fermentation differed among the treatments. High species diversity and various Gram-negative bacteria, such as Flavitalea sp., Pantoea agglomerans, Acinetobacter pittii, Turicibacter sanguinis, and Ralstonia pickettii, were found in the uninoculated LAB treatments. A beneficial bacterium, Lactobacillus johnsonii, was discovered for the first time in whole-plant paper mulberry silage. LAB inoculation simplifies the microbial community structure, and beneficial Lactobacillus as a key species aggregates in the inoculated treatment group. However, L. rhamnosus inoculation alone may have limited bacteriostatic activity against in whole-plant paper mulberry silage. Compared with silage lacking corn flour, amino sugar and nucleotide sugar metabolism, galactose metabolism, the phosphotransferase system and the pentose phosphate pathway metabolic activity were increased in corn flour-containing silage. Whole-plant paper mulberry can be used as a high-quality silage to provide high-quality feed resources for sustainable ruminant livestock production. Moreover, additive use is necessary for preparing paper mulberry silage.

Does Curing Moisture Content Affect Black Garlic Physiochemical Quality?

This research examined the changes of black garlic (BG) quality attributes when raw materials of different initial moisture contents (iMC) were used. Fresh garlic bulbs (cv. Thai) were shade-dried for eight weeks at a controlled condition at 29 °C and relative humidity (RH) of 55% to the desired iMC (ranging from ca. 50–70%). BG processing was at 75 °C, RH = 80% for ten days. After processing, physiological characteristics and chemical properties of garlic were determined. Results illustrated that fresh garlic with higher moisture content (ca. 70%) resulted in BG of a dark brown colour, sloppy texture, and lesser acidity (pH = 4.44), while samples with lower iMCs (<50%) gave products that were completely black, elastic in texture, and with higher acidity (pH = 3.79). The analysed bioactive compounds, as well as their antioxidative potentials, suggested that the longer the curing time, the higher the functional properties of the finished products, possessing a total phenolic, total flavonoid content, and antioxidant activity of 15.54 mg/kg dry matter sample, 1.53 mg/kg dry matter sample, and 95.39%, respectively. Principle component analysis (PCA) of active metabolites confirmed that sulfur, S-allyl-L-cysteine, and flavonoid were among the main phytochemicals found in the BG. In summary, higher quality BG can be achieved by using raw materials of lower iMC.

Pediococcus acidilactici Strains Improve Constipation Symptoms and Regulate Intestinal Flora in Mice

Constipation is a prevalent gastrointestinal disorder that seriously reduces the quality of life. Clinical studies have shown that a great change or severe imbalance occurs in the intestinal microbiota of people with constipation. This study explored whether bacteriocin-producing and non-bacteriocin-producing Pediococcus acidilactici strains resulted in differences in the alleviation of constipation and changes in the fecal flora in BALB/c mice. The constipation-related indicators, gastrointestinal regulatory peptides and gut microbiota were identified to evaluate their alleviating effects and underlying mechanisms. The time to the first black-stool defecation and the gastrointestinal transit rate in constipated mice were found to be somewhat improved by four P. acidilactici strains (P > 0.05). Moreover, there were significant differences in the level of most gastrointestinal regulatory peptides in the serum, as well as in the composition and abundance of intestinal microbiota in different groups (P < 0.05). At the phylum level, the relative abundance of Firmicutes was significantly increased, but those of Bacteroidetes and Proteobacteria were significantly reduced after the administration of four P. acidilactici strains for 14 d (P < 0.05). The levels of Bacteroides and genera from Enterobacteriaceae were significantly decreased, whereas Bifidobacterium and Lactobacillus were upregulated when bacteriocin-producing P. acidilactici CCFM18 and CCFM28 strains were provided in the diet (P < 0.05). The results indicated that although constipation-related symptoms were alleviated to only a limited degree, the administration of four P. acidilactici strains effectively regulated the gut flora and provided a potential health benefit to the host, especially the bacteriocin-producing P. acidilactici strains.

Omics approaches in Allium research: Progress and way ahead

BACKGROUND

The genus Allium (Family: Amaryllidaceae) is an economically important group of crops cultivated worldwide for their use as a vegetable and spices. Alliums are also well known for their nutraceutical properties. Among alliums, onion, garlic, leek, and chives cultivated worldwide. Despite their substantial economic and medicinal importance, the genome sequence of any of the Allium is not available, probably due to their large genome sizes. Recently evolved omics technologies are highly efficient and robust in elucidating molecular mechanisms of several complex life processes in plants. Omics technologies, such as genomics, transcriptomics, proteomics, metabolomics, metagenomics, etc. have the potential to open new avenues in research and improvement of allium crops where genome sequence information is limited. A significant amount of data has been generated using these technologies for various Allium species; it will help in understanding the key traits in Allium crops such as flowering, bulb development, flavonoid biosynthesis, male sterility and stress tolerance at molecular and metabolite level. This information will ultimately assist us in speeding up the breeding in Allium crops.

METHOD

In the present review, major omics approaches, and their progress, as well as potential applications in Allium crops, could be discussed in detail.

RESULTS

Here, we have discussed the recent progress made in Allium research using omics technologies such as genomics, transcriptomics, micro RNAs, proteomics, metabolomics, and metagenomics. These omics interventions have been used in alliums for marker discovery, the study of the biotic and abiotic stress response, male sterility, organ development, flavonoid and bulb color, micro RNA discovery, and microbiome associated with Allium crops. Further, we also emphasized the integrated use of these omics platforms for a better understanding of the complex molecular mechanisms to speed up the breeding programs for better cultivars.

CONCLUSION

All the information and literature provided in the present review throws light on the progress and potential of omics platforms in the research of Allium crops. We also mentioned a few research areas in Allium crops that need to be explored using omics technologies to get more insight. Overall, alliums are an under-studied group of plants, and thus, there is tremendous scope and need for research in Allium species.

Microbial Community Dynamics and Metabolome Changes During Spontaneous Fermentation of Northeast Sauerkraut From Different Households

Sauerkraut, one of the most popular traditional fermented vegetable foods in northern China, has been widely consumed for thousands of years. In this study, the physicochemical characteristics, microbial composition and succession, and metabolome profile were elucidated during the fermentation of traditional northeast sauerkraut sampled from different households. The microbial community structure as determined by high-throughput sequencing (HTS) technology demonstrated that Firmicutes and Proteobacteria were the predominant phyla and Weissella was the most abundant genus in all samples. Except for Weissella, higher relative abundance of Clostridium was observed in #1 sauerkraut, Clostridium and Enterobacter in #2 sauerkraut, and Lactobacillus in #3 sauerkraut, respectively. Meanwhile, Principal component analysis (PCA) revealed significant variances in the volatilome profile among different homemade sauerkraut. Acids and lactones were dominant in the #1 sauerkraut. The #2 sauerkraut had significantly higher contents of alcohols, aldehydes, esters, sulfides, and free amino acids (FAAs). In comparison, higher contents of terpenes and nitriles were found in the #3 sauerkraut. Furthermore, the potential correlations between the microbiota and volatilome profile were explored based on Spearman’s correlation analysis. Positive correlations were found between Clostridium, Enterobacter, Lactobacillus, Leuconostoc, Weissella and most volatile compounds. Pseudomonas, Chloroplast, Rhizobium, Aureimonas, and Sphingomonas were negatively correlated with volatile compounds in sauerkraut. This study provided a comprehensive picture of the dynamics of microbiota and metabolites profile during the fermentation of different homemade northeast sauerkraut. The elucidation of correlation between microbiota and volatile compounds is helpful for guiding future improvement of the fermentation process and manufacturing high-quality sauerkraut.

Deep insights into fungal diversity in traditional Chinese sour soup by Illumina MiSeq sequencing

Sour soup is a traditional condiment in Guizhou Province, China. The purpose of this study was to investigate the differences in the fungi present in 5 types of sour soup (tomato sour soup, chili sour soup, cherry tomato sour soup, spoiled tomato sour soup, and red sour soup made from blended tomato and chili sour soup subjected to secondary fermentation) and to determine the reasons for the deterioration of tomato sour soup by comparing the fungal communities in normal and deterioratedtomato sour soup. A total of 5 phyla were detected in all 5 samples, including Ascomycota (69.38%), Basidiomycota (7.63%), Zygomycota (1.59%), Chytridiomycota (0.01%) and unclassified phyla (21.39%). Ascomycota was the main phylum in each sample except the red sour soup made from blended tomato and chili sour soup subjected to secondary fermentation. That sour soup contained many unrecognized phyla. At the genus level, there were major differences among the different samples. Dekkera spp. and Pichia spp. were the main dominant fungus in tomato sour soup, Saccharomyces spp. and Pichia spp. were the dominant fungus in chili sour soup, and Pichia spp. were the dominant fungus in cherry tomato sour soup. When sour soup went bad, the fungus of sour soup changed greatly, and the unknown fungal genera, Cladospora spp., Saccharomyces spp. and Emericella spp. became the dominant fungal genera. In addition, after the secondary fermentation of tomato and chili sour soup mixed with garlic and ginger, the fungal genera of the base fermentation were replaced by unknown fungal genera. Moreover, there were various spoilage fungi in sour soup, which indicated that there were safety risks in naturally fermented sour soup and should be further controlled. This study revealed the fungal flora in sour soup made from different vegetables and compared the fungal diversity of spoiled and normal tomato sour soup and thereby provided a basis for understanding the fungal diversity of sour soup in China and guiding the production of sour soup.

Formation, nutritional value, and enhancement of characteristic components in black garlic: A review for maximizing the goodness to humans

Black garlic (BG) is essentially a processed food and obtained through the transformation of fresh garlic (FG) (Allium sativum L.) via a range of chemical reactions (including the Maillard reaction) and microbial fermentation. This review provides the up-to-date knowledge of the dynamic and complicated changes in major components during the conversion of FG to BG, including moisture, lipids, carbohydrates (such as sugars), proteins, organic acids, organic sulfur compounds, alkaloids, polyphenols, melanoidins, 5-hydroxymethylfurfural, vitamins, minerals, enzymes, and garlic endophytes. The obtained evidence confirms that BG has several advantages over FG in certain product attributes and biological properties (especially antioxidant activity), and the factors affecting the quality of BG include the type and characteristics of FG and processing technologies and methods (especially pretreatments, and processing temperature and humidity). The interactions among garlic components, and between garlic nutrients and microbes, as well as the interplay between pretreatment and main manufacturing process, all determine the sensory and nutritional qualities of BG. Before BG is marketed as a novel snack or functional food, more research is required to fill the knowledge gaps related to quantitative monitoring of the changes in metabolites (especially those taste-active and/or biological-active substances) during BG manufacturing to maximize BG's antioxidant, anticancer, antiobesity, anti-inflammatory, immunostimulatory, anti-allergic, hepatoprotective, cardioprotective and oxidative stress-/hangover syndrome-reducing functions, and beneficial effects on memory/nervous systems. Assessments of the quality, efficacy, and safety of BG should be performed considering the impacts of BG production conditions, postproduction handling, and intake methods.

Metagenomic data on bacterial diversity profiling of Arabian sea sediment by amplicon sequencing

This data is about the microbial community genome analysis of Arabian sea sediment by Illumina sequencing by targeting the hypervariable region V3 of 16S rRNA gene. The data analysis revealed the existence of numerous unknown sequences, indicating a large unexploited bacterial diversity in the area. The raw sequence data used for analysis is available in NCBI under the Sequence Read Archive (SRA) with the BioProject No. PRJNA397165 and SRA accession number SRP125840.