Metagenomic analysis revealed the potential of lactic acid bacteria in improving natural saline-alkali land / El análisis metagenómico reveló el potencial de las bacterias del ácido láctico para mejorar las tierras salino-álcalis naturales

Management and improving saline-alkali land is necessary for sustainable agricultural development. We conducted a field experiment to investigate the effects of spraying lactic acid bacteria (LAB) on the cucumber and tomato plant soils. Three treatments were designed, including spraying of water, viable or sterilized LAB preparations to the soils of cucumber and tomato plants every 20 days. Spraying sterilized or viable LAB could reduce the soil pH, with a more obvious effect by using viable LAB, particularly after multiple applications. Metagenomic sequencing revealed that the soil microbiota in LAB-treated groups had higher alpha-diversity and more nitrogen-fixing bacteria compared with the water-treated groups. Both viable and sterilized LAB, but not water application, increased the complexity of the soil microbiota interactive network. The LAB-treated subgroups were enriched in some KEGG pathways compared with water or sterilized LAB subgroups, such as environmental information processing–related pathways in cucumber plant; and metabolism-related pathways in tomato plant, respectively. Redundancy analysis revealed association between some soil physico-chemical parameters (namely soil pH and total nitrogen) and bacterial biomarkers (namely Rhodocyclaceae, Pseudomonadaceae, Gemmatimonadaceae, and Nitrosomonadales). Our study demonstrated that LAB is a suitable strategy for decreasing soil pH and improving the microbial communities in saline-alkali land.(AU)

Metagenomic analysis revealed the potential of lactic acid bacteria in improving natural saline-alkali land.

Management and improving saline-alkali land is necessary for sustainable agricultural development. We conducted a field experiment to investigate the effects of spraying lactic acid bacteria (LAB) on the cucumber and tomato plant soils. Three treatments were designed, including spraying of water, viable or sterilized LAB preparations to the soils of cucumber and tomato plants every 20 days. Spraying sterilized or viable LAB could reduce the soil pH, with a more obvious effect by using viable LAB, particularly after multiple applications. Metagenomic sequencing revealed that the soil microbiota in LAB-treated groups had higher alpha-diversity and more nitrogen-fixing bacteria compared with the water-treated groups. Both viable and sterilized LAB, but not water application, increased the complexity of the soil microbiota interactive network. The LAB-treated subgroups were enriched in some KEGG pathways compared with water or sterilized LAB subgroups, such as environmental information processing-related pathways in cucumber plant; and metabolism-related pathways in tomato plant, respectively. Redundancy analysis revealed association between some soil physico-chemical parameters (namely soil pH and total nitrogen) and bacterial biomarkers (namely Rhodocyclaceae, Pseudomonadaceae, Gemmatimonadaceae, and Nitrosomonadales). Our study demonstrated that LAB is a suitable strategy for decreasing soil pH and improving the microbial communities in saline-alkali land.

Intraspecific microdiversity and ecological drivers of lactic acid bacteria in naturally fermented milk ecosystem.

Traditional fermented milks are produced by inoculating technique, which selects well-adapted microorganisms that have been passed on through generations. Few reports have used naturally fermented milks as model ecosystems to investigate the mechanism of formation of intra-species microbial diversity. Here, we isolated and whole-genome-sequenced a total of 717 lactic acid bacterial isolates obtained from 12 independent naturally fermented milks collect from 12 regions across five countries. We further analyzed the within-sample intra-species phylogenies of 214 Lactobacillus helveticus isolates, 97 Lactococcus lactis subsp. lactis isolates, and 325 Lactobacillus delbrueckii subsp. bulgaricus isolates. We observed a high degree of intra-species genomic and functional gene diversity within-/between-sample(s). Single nucleotide polymorphism-based phylogenetic reconstruction revealed great within-sample intra-species heterogeneity, evolving from multiple lineages. Further phylogenetic reconstruction (presence-absence gene profile) revealed within-sample inter-clade functional diversity (based on carbohydrate-active enzyme- and peptidase-encoding genes) in all three investigated species/subspecies. By identifying and mapping clade-specific genes of intra-sample clades of the three species/subspecies to the respective fermented milk metagenome, we found extensive potential inter-/intra-species horizontal gene transfer events. Finally, the microbial composition of the samples is closely linked to the nucleotide diversity of the respective species/subspecies. Overall, our results contribute to the conservation of lactic acid bacteria resources, providing ecological insights into the microbial ecosystem of naturally fermented dairy products.

Bifidobacterium animalis subsp. lactis Probio-M8 undergoes host adaptive evolution by glcU mutation and translocates to the infant's gut via oral-/entero-mammary routes through lactation.

BACKGROUND: Most previous studies attempting to prove the phenomenon of mother-to-infant microbiota transmission were observational, performed only at genus/species-level resolution, and relied entirely on non-culture-based methodologies, impeding interpretation. RESULTS: This work aimed to use a biomarker strain, Bifidobacterium animalis subsp. lactis Probio-M8 (M8), to directly evaluate the vertical transmission of maternally ingested bacteria by integrated culture-dependent/-independent methods. Our culture and metagenomics results showed that small amounts of maternally ingested bacteria could translocate to the infant gut via oral-/entero-mammary routes through lactation. Interestingly, many mother-infant-pair-recovered M8 homologous isolates exhibited high-frequency nonsynonymous mutations in a sugar transporter gene (glcU) and altered carbohydrate utilization preference/capacity compared with non-mutant isolates, suggesting that M8 underwent adaptive evolution for better survival in simple sugar-deprived lower gut environments. CONCLUSIONS: This study presented direct and strain-level evidence of mother-to-infant bacterial transmission through lactation and provided insights into the impact of milk microbiota on infant gut colonization. Video Abstract.

Structure characterization, antioxidant and emulsifying capacities of exopolysaccharide derived from Tetragenococcus halophilus SNTH-8.

Tetragenococcus halophilus exopolysaccharides (THPS) are metabolites released by T. halophilus SNTH-8 to resist a high-salt environment. Although many studies have investigated the mechanisms underlying salt tolerance shown by T. halophilus, structural characteristics as well as antioxidant and emulsifying capacities of THPS remain unclear. In this study, we isolated and purified two components, THPS-1 and THPS-2, from T. halophilus SNTH-8. Purified THPS-1 and THPS-2 were composed of arabinose, xylose, fucose, galactose, glucose, and glucuronic acid at a molar ratio of 1.66:38.95:2.11:26.12:29.73:1.43 and 0.46:40.3:0.54:30.8:1.36:25.54, respectively. The average molecular weights of THPS-1 and THPS-2 were 14.98 kDa and 21.03 kDa, respectively. Moreover, the structures of THPS-1 and THPS-2 were investigated via fourier-transform infrared spectroscopy(FT-IR), nuclear magnetic resonance spectroscopy(NMR), scanning electron microscopy(SEM), and methylation analysis. THPS-1 was a highly branched polysaccharide with a backbone of α-D-(1,4)-Xyl, α-D-(1,6)-Glc and α-D-Xyl as the terminal, while THPS-2 was a highly branched polysaccharide with a backbone of α-D-(1,4)-Xyl and ß-D-GlcA as the terminal. The branches were identified as ß-D-(1,4,6)-Gal and ß-D-(1,6)-Gal. Both THPS-1 and THPS-2 exhibited high antioxidant and emulsifying capacities. Overall, our structural analysis of THPS may further enhance research on natural emulsifiers and antioxidants.

Comparative genomic analysis of 455 Lactiplantibacillus plantarum isolates: Habitat-specific genomes shaped by frequent recombination.

A large-scale comparative genomic analysis together with genome-wide association study of 455 Lactiplantibacillus (L.) plantarum genomes was performed. Firstly, the study generated phylogenic tree using core-genome of L. plantarum, and the phylogenetic tree comprised two major clades. The isolates in clade B were genetically more diverse than those of clade A. Furthermore, a mono-clade (clade B1) of 12 isolates was identified within clade B in L. plantarum. It is interesting to note that these 12 isolates were originated from diverse niches and wide geographic regions. Plant-associated isolates were distributed evenly across the phylogenetic tree. In contrast, more dairy product-originated isolates were distributed in clade B, while the animal- and meat product-originated isolates located mainly in clade A. The overall r/m ratio (ratio of recombination and mutation events) of all 455 L. plantarum isolates (1.181) was a lot lower than that of clade B1 (5.510), and there was a seven-fold difference in the r/m ratio between animal-originated isolates distributed to clade A (0.607) and clade B (4.373). The dairy and animal-originated isolates possessed multiple environment-specific genes. Our findings deepen the understanding of the niche-specific genome diversity of L. plantarum.

Study on Streptococcus thermophilus isolated from Qula and associated characteristic of acetaldehyde and diacetyl in their fermented milk.

In this study, the lactic acid bacterial population of Qula cheese from the Gansu and Sichuan provinces of China were isolated and identified. Eight strains of Streptococcus thermophilus were isolated, of which five strains were selected for further characterization based on their fermentation properties. The changes in a number of parameters, including titration acidity, pH, viable counts, PrtS protease activity and the production of acetaldehyde, diacetyl and organic acid, were monitored during fermentation and the storage of fermented milks produced by the respective strain. All of the strains displaying acidifying capacity and all five fermented milks maintained high viable counts of S. thermophilus from fermentation to storage. Our study found that the changes in the monitored parameters were strain-specific and varied considerably among the five tested strains. Fermented milks produced by strain IMAU80809 had the highest concentration of acetaldehyde and were most favorable in the sensory evaluation. This study confirms that Qula cheese is a good source for isolating novel lactic acid bacterial strains with different fermentation properties, which will be very useful for further development and industrialization of traditionally fermented dairy products.

Population structure of Lactobacillus helveticus isolates from naturally fermented dairy products based on multilocus sequence typing.

Lactobacillus helveticus is an economically important lactic acid bacterium used in industrial dairy fermentation. In the present study, the population structure of 245 isolates of L. helveticus from different naturally fermented dairy products in China and Mongolia were investigated using an multilocus sequence typing scheme with 11 housekeeping genes. A total of 108 sequence types were detected, which formed 8 clonal complexes and 27 singletons. Results from Structure, SplitsTree, and ClonalFrame software analyses demonstrated the presence of 3 subpopulations in the L. helveticus isolates used in our study, namely koumiss, kurut-tarag, and panmictic lineages. Most L. helveticus isolates from particular ecological origins had specific population structures.

Complete genome sequence of probiotic Lactobacillus plantarum P-8 with antibacterial activity.

Lactobacillus plantarum P-8 is a probiotic bacterium, which shows high antibacterial activity. The genome consists of a circular 3,033,693-bp chromosome and six plasmids. Bioinformatics inspection of the genome revealed a gene cluster relating to bacteriocin production. Genome information has provided the basis for understanding the potential molecular mechanism behind the bacteriocin production.

Complete genome sequence of the probiotic Lactobacillus fermentum F-6 isolated from raw milk.

Lactobacillus fermentum F-6 was isolated from raw milk in Inner Mongolia of China with desirable probiotic properties. The genome contains a circular 2.06Mb chromosome and has no plasmid. Further in silico analysis revealed its genetic basis for adhesion, exopolysaccharides production and citrate fermentation, which makes it a strain of high industrial potential.

Angiotensin-converting enzyme inhibitory activity of Lactobacillus helveticus strains from traditional fermented dairy foods and antihypertensive effect of fermented milk of strain H9.

Hypertension is a major global health issue which elevates the risk of a large world population to chronic life-threatening diseases. The inhibition of angiotensin-converting enzyme (ACE) is an effective target to manage essential hypertension. In this study, the fermentation properties (titratable acidity, free amino nitrogen, and fermentation time) and ACE-inhibitory (ACEI) activity of fermented milks produced by 259 Lactobacillus helveticus strains previously isolated from traditional Chinese and Mongolian fermented foods were determined. Among them, 37 strains had an ACEI activity of over 50%. The concentrations of the antihypertensive peptides, Ile-Pro-Pro and Val-Pro-Pro, were further determined by ultra performance liquid chromatography with quadrupole-time-of-flight mass spectrometry. The change of ACEI activity of the fermented milks of 3 strains exhibiting the highest ACEI activity upon gastrointestinal protease treatment was assayed. Fermented milks produced by strain H9 (IMAU60208) had the highest in vitro ACEI activity (86.4 ± 1.5%), relatively short fermentation time (7.5 h), and detectable Val-Pro-Pro (2.409 ± 0.229 µM) and Ile-Pro-Pro (1.612 ± 0.114 µM) concentrations. Compared with the control, a single oral dose of H9-fermented milk significantly attenuated the systolic, diastolic, and mean blood pressure of spontaneously hypertensive rats (SHR) by 15 to 18 mmHg during the 6 to 12 h after treatment. The long-term daily H9-fermented milk intake over 7 wk exerted significant antihypertensive effect to SHR, but not normotensive rats, and the systolic and diastolic blood pressure were significantly lower, by 12 and 10 mmHg, respectively, compared with the control receiving saline. The feeding of H9-fermented milk to SHR resulted in a significantly higher weight gain at wk 7 compared with groups receiving saline, commercial yogurt, and captopril. Our study identified a novel probiotic L. helveticus strain originated from kurut sampled from Tibet (China), which is a valuable resource for future development of functional foods for hypertension management.

Isolation and identification of lactic acid bacteria from Tarag in Eastern Inner Mongolia of China by 16S rRNA sequences and DGGE analysis.

Tarag is a characteristic fermented dairy product with rich microflora (especially lactic acid bacteria), developed by the people of Mongolian nationality in Inner Mongolia of China and Mongolia throughout history. One hundred and ninety-eight samples of Tarag were collected from scattered households in Eastern Inner Mongolia, and total of 790 isolates of lactic acid bacteria (LAB) were isolated by traditional pure culture method. To identify these isolates and analyze their biodiversity, 16S rRNA gene sequences analysis and PCR-DGGE were performed respectively. The results showed that 790 isolates could be classified as 31 species and subspecies. Among these isolates, Lactobacillus helveticus (153 strains, about 19.4%), Lactococcus lactis subsp. lactis (132 strains, about 16.7%) and Lactobacillus casei (106 strains, about 11.0%) were considered as the predominated species in the traditional fermented dairy products (Tarag) in Eastern Inner Mongolia. It was shown that the biodiversity of LAB in Tarag in Inner Mongolia was very abundant, and this traditional fermented dairy product could be considered as valuable resources for LAB isolation and probiotic selection.