Using PacBio Long-Read High-Throughput Microbial Gene Amplicon Sequencing To Evaluate Infant Formula Safety

Composition and factors influencing community structure of lactic acid bacterial in dairy products from Nyingchi Prefecture of Tibet

This study investigated the community composition of lactic acid bacteria (LAB) from yaks' milk (YM) Tibetan yellow cattle milk (TM) and their fermented products from different counties in the Nyingchi Prefecture, Tibet using Pacific Biosciences (PacBio) single-molecule real-time (SMRT) sequencing. Sequencing revealed 26 genera and 94 species from 71 dairy samples; amongst these Lactobacillus delbrueckii (36.17%), Streptococcus thermophilus (19.46%) and Lactococcus lactis (18.33%) were the predominant species. This study also identified the main factors influencing LAB community composition by comparing amongst samples from different locations, from different milk types, and from different altitudes. The LAB communities in YM and TM were more diverse than in fermented yaks' milk (FYM) and fermented Tibetan yellow cattle milk (FTM) samples. Similarly, whether milk was fermented or not accounted for differences in LAB species composition while altitude of the dairy products had very little effect. Milk source and production process were the most likely causes of drastic shifts in microbial community composition. In addition, fermented dairy products were enriched in genes responsible for secondary metabolic pathways that were potentially beneficial for health. Comprehensive descriptions of the microbiota in different dairy products from the Nyingchi Prefecture, Tibet might help elucidate evolutionary and functional relationships amongst bacterial communities in these products.

A new Leuconostoc citreum strain discovered in the traditional sweet potato sour liquid fermentation as a novel bioflocculant for highly efficient starch production

Sour liquid fermentation is commonly used in the sedimentation process of traditional starch production, where bacteria play a critical role in starch flocculation. In this study, the dynamic changes of bacterial compositions during sweet potato sour liquid (SPSL) fermentation were profiled using the single-molecule real-time (SMRT) sequencing, unveiling that Leuconostoc citreum, Leuconostoc pseudomesenteroides, Lactococcus lactis, and Lactobacillus plantarum were the dominant microorganisms in the process, and Leuconostoc citreum exhibited a strong positive correlation with starch flocculation rate (FR). In total, 75 lactic acid bacterial (LAB) strains were isolated from the SPSL, but only 7 of them caused starch flocculation. For the first time, Leuconostoc citreum strains were reported with excellent starch-flocculating abilities (up to 55.56% FR in 20 min), which might be attributed to their ability to connect starch granules through the cell surface to form large aggregation. This study provides a comprehensive understanding of the bacterial dynamics in SPSL fermentation at the species level. A starch flocculation yield of 93.63% was achieved within 1 h by using the newly discovered Leuconostoc citreum SJ-57. The time required for total starch sedimentation was reduced from 10 h to 4 h, compared with the traditional process. These results suggest that this novel bioflocculant is more suitable for modernizing the traditional SPSL fermentation process and achieving rapid and highly efficient starch sedimentation.

Comparison of Bacterial Microbiota in Raw Mare's Milk and Koumiss Using PacBio Single Molecule Real-Time Sequencing Technology

Koumiss is a traditional fermented raw mare’s milk product. It contains high nutritional value and is well-known for its health-promoting effect as an alimentary supplement. This study aimed to investigate the bacterial diversity, especially lactic acid bacteria (LAB), in koumiss and raw mare’s milk. Forty-two samples, including koumiss and raw mare’s milk, were collected from the pastoral area in Yili, Kazakh Autonomous Prefecture, Xinjiang Uygur Autonomous Region in China. This work applied PacBio single-molecule real-time (SMRT) sequencing to profile full-length 16S rRNA genes, which was a powerful technology enabling bacterial taxonomic assignment to the species precision. The SMRT sequencing identified 12 phyla, 124 genera, and 227 species across 29 koumiss samples. Eighteen phyla, 286 genera, and 491 species were found across 13 raw mare’s milk samples. The bacterial microbiota diversity of the raw mare’s milk was more complex and diverse than the koumiss. Raw mare’s milk was rich in LAB, such as Lactobacillus (L.) helveticus, L. plantarum, Lactococcus (Lc.) lactis, and L. kefiranofaciens. In addition, raw mare’s milk also contained sequences representing pathogenic bacteria, such as Staphylococcus succinus, Acinetobacter lwoffii, Klebsiella (K.) oxytoca, and K. pneumoniae. The koumiss microbiota mainly comprised LAB, and sequences representing pathogenic bacteria were not detected. Meanwhile, the koumiss was enriched with secondary metabolic pathways that were potentially beneficial for health. Using a Random Forest model, the two kinds of samples could be distinguished with a high accuracy 95.2% [area under the curve (AUC) = 0.98] based on 42 species and functions. Comprehensive depiction of the microbiota in raw mare’s milk and koumiss might help elucidate evolutionary and functional relationships among the bacterial communities in these dairy products. The current work suffered from the limitation of a low sample size, so further work would be required to verify our findings.

Streamlining Quantitative Analysis of Long RNA Sequencing Reads

Transcriptome analyses allow for linking RNA expression profiles to cellular pathways and phenotypes. Despite improvements in sequencing methodology, whole transcriptome analyses are still tedious, especially for methodologies producing long reads. Currently, available data analysis software often lacks cost- and time-efficient workflows. Although kit-based workflows and benchtop platforms for RNA sequencing provide software options, e.g., cloud-based tools to analyze basecalled reads, quantitative, and easy-to-use solutions for transcriptome analysis, especially for non-human data, are missing. We therefore developed a user-friendly tool, termed Alignator, for rapid analysis of long RNA reads requiring only FASTQ files and an Ensembl cDNA database reference. After successful mapping, Alignator generates quantitative information for each transcript and provides a table in which sequenced and aligned RNA are stored for further comparative analyses.

Short communication: Dynamic changes in bacterial diversity during the production of powdered infant formula by PCR-DGGE and high-throughput sequencing

Microorganisms such as thermophilic and psychrotrophic bacteria cause spoilage of milk and milk products [e.g., powdered infant formula (PIF)], mainly because they produce heat-stable extracellular enzymes. However, the dynamic changes in microbial diversity during PIF production are still not well understood. We used denaturing gradient gel electrophoresis (DGGE) and high-throughput sequencing (HTS) to investigate bacterial community structure and distribution during the major stages of PIF production: raw milk, pasteurization, mixing, evaporation, and spray-drying. Our PCR-DGGE analysis indicated that Lactobacillus and Pseudomonas spp. were the dominant bacteria at the raw milk and pasteurization stages; Lactococcus, Streptococcus, Enterococcus, and Lactobacillus spp. were abundant during mixing, evaporation, and spray-drying. Our HTS analysis showed that Pseudomonas had an abundance of 96.79% at the raw milk stage. Lactobacillus, Streptococcus, Thermus, Acinetobacter, and Bacteroides spp. were most common after pasteurization. The index of bacterial diversity was highest at the evaporation stage, suggesting a high potential risk of microbial contamination. The results from DGGE and HTS were consistent in reflecting changes in dominant flora, but different in reflecting the richness of bacterial communities present during PIF production: HTS revealed a much higher richness of bacterial species than DGGE. Our findings from DGGE and HTS showed that psychrophilic and thermophilic bacteria were the main flora present during PIF production: psychrophilic bacteria were mainly Pseudomonas spp. and thermophilic bacteria were mainly Lactobacillus, Streptococcus, and Bacillus spp. To our knowledge, this is the first study to report dynamic changes in microbial communities during PIF production. Our results provide insight into bacterial communities and identify potential contamination sources that could serve as a guide for reducing microbial risk.

Profiling of the viable bacterial and fungal microbiota in fermented feeds using single-molecule real-time sequencing

Fermented concentrated feed has been widely recognized as an ideal feed in the animal industry. In this study, we used a powerful method, coupling propidium monoazide (PMA) pretreatment with single-molecule real-time (SMRT) sequencing technology to compare the bacterial and fungal composition of feeds before and after fermentation with four added lactic acid bacteria (LAB) inoculants (one Lactobacillus casei strain and three L. plantarum strains). Five feed samples consisting of corn, soybean meal, and wheat bran were fermented with LAB additives for 3 d. Following anaerobic fermentation, the pH rapidly decreased, and the mean numbers of LAB increased from 106 to 109 colony-forming units (cfu)/g fresh matter. SMRT sequencing results showed that the abundance and diversity of bacteria and fungi in the feed were significantly higher before fermentation than after fermentation. Fifteen bacterial species and eight fungal genera were significantly altered following fermentation, and L. plantarum was the dominant species (relative abundance 88.94%) in the post-fermentation group. PMA treatment revealed that the bacteria Bacillus cereus, B. circulans, Alkaliphilus oremlandii, Cronobacter sakazakii, Paenibacillus barcinonensis, and P. amylolyticus (relative abundance >1%) were viable in the raw feed. After fermentation, their relative abundances decreased sharply to <0.2%; however, viable L. plantarum was still the dominant species post fermentation. We inferred that our LAB additives grew rapidly and inhibited harmful microorganisms and further improved feed quality. In addition, coupling PMA treatment with the Pacific Biosciences SMRT sequencing technology was a powerful tool for providing accurate live microbiota profiling data in this study.

Lactobacillus casei protects dextran sodium sulfate- or rapamycin-induced colonic inflammation in the mouse

PURPOSE

Human colon inflammation is associated with changes in the diverse and abundant microorganisms in the gut. As important beneficial microbes, Lactobacillus contributes to the immune responses and intestinal integrity that may alleviate experimental colitis. However, the mechanisms underlying probiotic benefits have not been fully elucidated.

METHODS

Dextran sodium sulfate or rapamycin-challenged mice were used as model for colon inflammation evaluation. Histological scores of the colon, levels of colonic myeloperoxidase, serum tumor necrosis factor-α and interleukin-6 were assessed as inflammatory markers and the gut microbiota profiles of each mouse were studied.

RESULTS

We found that Lactobacillus casei Zhang (LCZ) can prevent experimental colitis and rapamycin-induced inflammation in intestinal mucosa by improving histological scores, decreasing host inflammatory cytokines, modulating gut-dominated bacteria, enhancing cystic fibrosis transmembrane conductance regulator (CFTR) expression and downregulating the expression of p-STAT3 (phosphorylated signal transducer and activator of transcription 3) or Akt/NF-κB (AKT serine/threonine kinase and nuclear factor kappa B).

CONCLUSION

Our results suggest that LCZ may provide effective prevention against colitis.

Oral Administration of Compound Probiotics Improved Canine Feed Intake, Weight Gain, Immunity and Intestinal Microbiota

Probiotics have been used successfully to promote human and animal health, but only limited studies have focused on using probiotics to improve the health of hosts of different age. Canine microbiome studies may be predictive of results in humans because of the high structural and functional similarity between dog and human microbiomes. A total of 90 dogs were divided into three groups based on dog age (elderly group, n = 30; young group, n = 24; and training group, n = 36). Each group was subdivided into two subgroups, with and without receiving daily probiotic feed additive. The probiotic feed additive contained three different bacterial strains, namely Lactobacillus casei Zhang, Lactobacillus plantarum P-8, and Bifdobacterium animalis subsp. lactis V9. Serum and fecal samples were collected and analyzed at four different time points, i.e., days 0, 30, and 60 of probiotic treatment, and 15 days after ceasing probiotic treatment. The results demonstrated that probiotics significantly promoted the average daily feed intake of the elderly dogs (P < 0.01) and the average daily weight gain of all dogs (P < 0.05), enhanced the level of serum IgG (P < 0.001), IFN-α (P < 0.05), and fecal SIgA (P < 0.001), while reduced the TNF-α (P < 0.05). Additionally, probiotics could change the gut microbial structure of elderly dogs and significantly increased beneficial bacteria (including some Lactobacillus species and Faecalibacterium prausnitzii) and decreased potentially harmful bacteria (including Escherichia coli and Sutterella stercoricanisin), and the elderly dogs showed the strongest response to the probiotics; the relative abundance of some of these species correlated with certain immune factors and physiological parameters, suggesting that the probiotic treatment improved the host health and enhanced the host immunity by stimulating antibody and cytokine secretion through regulating canine gut microbiota. Furthermore, the gut microbiota of the elderly dogs shifted toward a younger-like composition at day 60 of probiotic treatment. Our findings suggested that the probiotic treatment effects on canine health and immunity were age-related and have provided interesting insights into future development of probiotic-based strategies to improve animal and human health.

Evaluation of Bacterial Contamination in Goat Milk Powder Using PacBio Single Molecule Real-Time Sequencing and Droplet Digital PCR

Goat milk powder is a nutritious and easy-to-store product that is highly favored by consumers. However, the presence of contaminating bacteria and their metabolites may significantly affect the flavor, solubility, shelf life, and safety of the product. To comprehensively and accurately understand the sanitary conditions in the goat milk powder production process and potential threats from bacterial contamination, a combination of Pacific Biosciences single molecule real-time sequencing and droplet digital PCR was used to evaluate bacterial contamination in seven goat milk powder samples from three dairies. Ten phyla, 119 genera, and 249 bacterial species were identified. Bacillus, Paenibacillus, Lactococcus, and Cronobacter were the primary genera. Bacillus cereus, Lactococcus lactis, Alkaliphilus oremlandii, and Cronobacter sakazakii were the dominant species. With droplet digital PCR, 6.3 × 10⁴ copies per g of Bacillus cereus and 1.0 × 10⁴ copies per g of Cronobacter spp. were quantified, which may increase the risk of food spoilage and the probability of foodborne illness and should be monitored and controlled. This study offers a new approach for evaluating bacterial contamination in goat milk powder and supplies a reference for the assessment of food safety and control of potential risk, which will be of interest to the dairy industry.

Bacterial Microbiota and Metabolic Character of Traditional Sour Cream and Butter in Buryatia, Russia

Traditional sour cream and butter are widely popular fermented dairy products in Russia for their flavor and nutrition, and contain rich microbial biodiversity, particularly in terms of lactic acid bacteria (LAB). However, few studies have described the microbial communities and metabolic character of traditional sour cream and butter. The objective of this study was to determine the bacterial microbiota and metabolic character of eight samples collected from herdsmen in Buryatia, Russia. Using single-molecule real-time (SMRT) sequencing techniques, we identified a total of 294 species and/or subspecies in 169 bacterial genera, belonging to 14 phyla. The dominant phylum was Firmicutes (81.47%) and the dominant genus was Lactococcus (59.28%). There were differences between the bacterial compositions of the sour cream and butter samples. The relative abundances of Lactococcus lactis, Lactococcus raffinolactis, and Acetobacter cibinongensis were significantly higher in sour cream than in butter, and the abundance of Streptococcusthermophilus was significantly lower in sour cream than in butter. Using a pure culture method, 48 strains were isolated and identified to represent seven genera and 15 species and/or subspecies. Among these isolates, Lactococccus lactis subsp. lactis (22.50%) was the dominant LAB species. Ultra-performance liquid chromatography–quadrupole–time of flight mass spectrometry at elevated energy was used in combination with statistical methods to detect metabolite differences between traditional sour cream and butter. A total of 27,822 metabolites were detected in all samples, and Lys-Lys, isohexanal, palmitic acid, Leu-Val, and 2′-deoxycytidine were the most dominant metabolites found in all samples. In addition, 27 significantly different metabolites were detected between the sour cream and butter samples, including short peptides, organic acids, and amino acids. Based on correlation analyses between the most prevalent bacterial species and the main metabolites in sour cream, we conclude that there may be a connection between the dominant LAB species and these metabolites. This study combined omics techniques to analyze the bacterial diversity and metabolic character of traditional sour cream and butter, and we hope that our findings will enrich species resource libraries and provide valuable resources for further research on dairy product flavor.

Using PacBio sequencing to investigate the bacterial microbiota of traditional Buryatian cottage cheese and comparison with Italian and Kazakhstan artisanal cheeses

Traditional fermented dairy foods including cottage cheese have been major components of the Buryatia diet for centuries. Buryatian cheeses have maintained not only their unique taste and flavor but also their rich natural lactic acid bacteria (LAB) content. However, relatively few studies have described their microbial communities or explored their potential to serve as LAB resources. In this study, the bacterial microbiota community of 7 traditional artisan cheeses produced by local Buryatian families was investigated using single-molecule, real-time sequencing. In addition, we compared the bacterial microbiota of the Buryatian cheese samples with data sets of cheeses from Kazakhstan and Italy. Furthermore, we isolated and preserved several LAB samples from Buryatian cheese. A total of 62 LAB strains (belonging to 6 genera and 14 species or subspecies) were isolated from 7 samples of Buryatian cheese. Full-length 16S rRNA sequencing of the microbiota revealed 145 species of 82 bacterial genera, belonging to 7 phyla. The most dominant species was Lactococcus lactis (43.89%). Data sets of cheeses from Italy and Kazakhstan were retrieved from public databases. Principal component analysis and multivariate ANOVA showed marked differences in the structure of the microbiota communities in the cheese data sets from the 3 regions. Linear discriminant analyses of the effect size identified 48 discriminant bacterial clades among the 3 groups, which might have contributed to the observed structural differences. Our results indicate that the bacterial communities of traditional artisan cheeses vary depending on geographic origin. In addition, we isolated novel and valuable LAB resources for the improvement of cottage cheese production.

Evaluation of different 16S rRNA gene V regions for exploring bacterial diversity in a eutrophic freshwater lake

Massive partial sequencing of 16S rRNA genes has become the predominant tool used for studying microbial ecology. However, determining which hypervariable regions and primer sets should be used for screening microbial communities requires extensive investigation if controversial results are to be avoided. Here, the performances of different variable regions of the 16S rRNA gene on bacterial diversity studies were evaluated in silico with respect to the SILVA non-redundant reference database (SILVA SSU Ref 123NR), and subsequently verified using samples from Lake Taihu in China, a eutrophic lake. We found that the bacterial community composition results were strongly impacted by the different V regions. The results show that V1-V2 and V1-V3 regions were the most reliable regions in the full-length 16S rRNA sequences, while most V3 to V6 regions (including V3, V4, V3-V4, V5, V4-V5, V6, V3-V6, V4-V6, and V5-V6) were more closely aligned with the SILVA SSU Ref 123NR database. Overall, V4 was the most prominent V region for achieving good domain specificity, higher coverage and a broader spectrum in the Bacteria domain, as confirmed by the validation experiments. S-D-Bact-0564-a-S-15/S-D-Bact-0785-b-A-18 is, therefore, a promising primer set for surveying bacterial diversity in eutrophic lakes.

A Novel Lactobacilli-Based Teat Disinfectant for Improving Bacterial Communities in the Milks of Cow Teats with Subclinical Mastitis

Teat disinfection pre- and post-milking is important for the overall health and hygiene of dairy cows. The objective of this study was to evaluate the efficacy of a novel probiotic lactobacilli-based teat disinfectant based on changes in somatic cell count (SCC) and profiling of the bacterial community. A total of 69 raw milk samples were obtained from eleven Holstein-Friesian dairy cows over 12 days of teat dipping in China. Single molecule, real-time sequencing technology (SMRT) was employed to profile changes in the bacterial community during the cleaning protocol and to compare the efficacy of probiotic lactic acid bacteria (LAB) and commercial teat disinfectants. The SCC gradually decreased following the cleaning protocol and the SCC of the LAB group was slightly lower than that of the commercial disinfectant (CD) group. Our SMRT sequencing results indicate that raw milk from both the LAB and CD groups contained diverse microbial populations that changed over the course of the cleaning protocol. The relative abundances of some species were significantly changed during the cleaning process, which may explain the observed bacterial community differences. Collectively, these results suggest that the LAB disinfectant could reduce mastitis-associated bacteria and improve the microbial environment of the cow teat. It could be used as an alternative to chemical pre- and post-milking teat disinfectants to maintain healthy teats and udders. In addition, the Pacific Biosciences SMRT sequencing with the full-length 16S ribosomal RNA gene was shown to be a powerful tool for monitoring changes in the bacterial population during the cleaning protocol.