SMRT sequencing and ddPCR reveal the complexity of developmental trajectories and temporal dynamics of gut bifidobacterial communities in infants

Infant intestinal microbiome is closely linked with health and risk of disease. Bifidobacterium are important components of the infant gut and are known to confer various health effects on the host. However, few studies have described the precise composition and dynamics of early infant gut bifidobacterial communities. Thus, this was a pilot study aiming to describe the developmental trajectories and temporal dynamics of bifidobacterial communities in infants before 6 months of age. A total of 28 fecal samples from 4 infants(GF, ZZ, QM, TN, respectively)were collected and analyzed after 5, 15, 30, 60, 90, 120, 150, and 180 days of birth by a bifidobacteria-target method(based on single-molecule real-time sequencing of partial bifidobacterial rpsK genes)in conjunction with droplet digital polymerase chain reaction(ddPCR). The infant fecal microbiota comprised a total of 11 bifidobacterial species, including 4 major species, i.e., B. dentium(37.35%), B. catenulatum(32.04%), B. breve(22.24%), and B. animalis(8.02%). The infant microbiota showed highly individualized developmental trajectories. The leading species for GF was B. catenulatum, with a relatively stable developmental trajectory. In ZZ, B. breve was enriched, and the developmental trajectory was rather fluctuating. The most abundant species for QM and TN was B. dentium. The developmental trajectory of B. dentium in QM showed a trend of gradual decrease, whereas an opposite trend was seen in samples of TN. The results of ddPCR confirmed large variations in quantities of bifidobacteria between infants and suggested discordances in temporal dynamics of bifidobacterial communities during the first half year of infancy. In conclusion, our results suggested that the early infant gut bifidobacterial microbiota was highly complex and temporal dynamics, with individualized developmental trajectories, which should be considered in future research of infant gut microbiota.

Effects of probiotics and its fermented milk on constipation: a systematic review

This study reviewed clinical evidence of probiotics-mediated effects on constipation.Four databases were used in the literature searches,namely Cochrane Library,Embase,Pubmed,and Web of Science.The last retrieval time was March 2021.Collected data were analyzed by Review Manager(version 5.3)and Stata(version 14).The primary search retrieved 8418 articles after removing duplicates.Eventually,26 studies were included in the meta-analysis.Administration of probiotics signifi cantly increased stool frequency(MD:1.15 times/week;95%CI:0.59 to 1.70;P<0.0001),improved bloating(MD:-0.48;95%CI:-0.89 to-0.07;P=0.02),reduced abdominal pain(MD:-0.71;95%CI:-1.25 to-0.16;P=0.01),and improved quality of life(MD:-0.73;95%CI:-1.37 to-0.10;P=0.02).However,the clinical effect of intake of probiotics on stool consistency was non-signifi cant(MD:0.07;95%CI:-0.34 to 0.48;P=0.73).Based on our analysis,probiotic supplements were effective in relieving constipation through symptom improvement.The effectiveness of dosage forms of intervention ranked:capsules>others(tablets,powder)>fermented milk.

Lacticaseibacillus rhamnosus Probio-M9 may be vertically transmitted from mother to infant during lactation based on faeces metagenomics

Probiotics exert beneficial effects on the host.This study aimed to investigate whether maternally ingested Lacticaseibacillus rhamnosus Probio-M9 during pregnancy could access and colonize the infant gut.This study recruited one pregnant woman,who ingested Probio-M9 daily from 35 weeks of gestation to delivery.Feces of the mother-infant pair were regularly collected from one month before delivery to 6 months of infant's age for metagenomic sequencing.Probio-M9 genomes were mappable to all infant fecal samples,suggesting the ingested probiotics could be vertically transmitted from mother to infant.Infant-or mother-specific differential metabolic pathways were found between the maternal and infant's gut microbiome,implicating apparent differences in the intestinal metagenomic potential/function between the mother and the infant.In conclusion,maternal ingestion of Probio-M9 during the final weeks of gestation could deliver to the infant gut.The findings provided novel insights into shaping infant's gut microbiota.

Koumiss Consumption Alleviates Symptoms of Patients with Chronic Atrophic Gastritis:A Possible Link to Modulation of Gut Microbiota

Intestinal dysbiosis is closely related to a variety of medical conditions,especially gastrointestinal diseases.The present study aimed to investigate the effects of koumiss on chronic atrophic gastritis(CAG)in an outpatient clinical trial(n=10;all female subjects aged 41-55;body mass index ranging from 19.5 to 25.8).Each patient consumed three servings of koumiss per day(i.e.250 ml daily before each of 3 meals)for a 60-day period.The improvement of patients'symptoms was monitored by comparing the total scores of symptoms before and after the treatment.Meanwhile,the changes in the patients’fecal microbiota composition and specific blood parameters were determined.After the 60-day koumiss administration,significant symptom improvements were observed,as evidenced by the reduction of the total symptoms score,and changes in blood platelet and cholesterol levels.The changes in patients’fecal microbiota composition were found.The patients’fecal microbiota fell into two distinct enterotypes,Bacteroides dorei/Bacteroides uniformis(BB-enterotype)and Prevotella copri(P-enterotype).Significant less Bacteroides uniformis was found in the BB-enterotype patient group,while significant more butyrate-producing bacteria(e.g.Eubacterium rectale and Faecalibacterium prausnitzii)were found in the P-enterotype patient group,following koumiss administration.After stopping koumiss consumption,the relative abundance of some biomarker taxa returned to the original level,suggesting that the gut microbiota modulatory effect was not permanent and that continuous koumiss administration was required to maintain the therapeutic effect.In conclusion,koumiss consumption could alleviate the symptoms of CAG patients.Our results may help understand the mechanism of koumiss in alleviating CAG disease symptoms,facilitating the development of such products with desired therapeutic functions.

Colloidal nanoparticles prepared from zein and casein:interactions,characterizations and emerging food applications

Protein colloidal nanoparticles(NPs)are ubiquitous present in nature and function as building blocks with multiple functions in both food formulations and biological processes.Food scientists are inspired by naturally occurring proteins to induce self-assembly behavior of protein by manipulating environmental parameters,providing opportunities to construct special and expected NPs.Zein and casein,the main proteins derived from corn and milk,are two examples of the most prevalently studied food proteins for nanoarchitectures in recent years.In this article,the compositions,structures,and physicochemical properties of these two proteins and casein derivatives are summarized as well as their interactions and characterizations.Strategies to fabricate zein-sodium caseinate based NPs are critically highlighted and illustrated.Particularly,applications such as encapsulation and delivery of bioactive compounds,producing food packaging for enhanced antioxidative and antimicrobial effects,and stabilization of emulsions to achieve fat replacement.Due to the imperative role of food proteins in diet composition,this review not only provides cutting-edge knowledge for nanoparticle construction but also opens new avenues for efficient utilization and exploitation of food proteins.

Spraying compound probiotics improves growth performance and immunity and modulates gut microbiota and blood metabolites of suckling piglets

One factor that shapes the establishment of early neonatal intestinal microbiota is environmental microbial exposure,and probiotic application has been shown to promote health and growth of piglets.Thus,this study hypothesized that environmental probiotic application in early days of life would be beneficial to newborn piglets.This study aimed to investigate the effect of spraying a compound probiotic fermented liquid(CPFL)into the living environment of piglets on their early growth performance and immunity.This work included 68 piglets,which were randomized into probiotic and control groups.Blood and fecal samples were collected at 0,3,7,14,and 21 days of age.Spraying CPFL significantly reshaped the microbiota composition of the delivery room environment,increased piglets’daily weight gain and weaning weight(P<0.001),and modulated piglets’serum cytokine levels(increases in Ig A,Ig G,and IL-10;decrease in IFN-γ;P<0.05 in each case)in piglets.Additionally,spraying CPFL during early days of life modified piglets’gut microbiota structure and diversity,increased the abundance of some potentially beneficial bacteria(such as Bacteroides uniformis,Butyricimonas virosa,Parabacteroides distasonis,and Phascolarctobacterium succinatutens)and decreased the abundance of Escherichia coli(P<0.05).Interestingly,CPFL application also significantly enhanced the gut microbial bioactive potential and levels of several serum metabolites involved in the metabolism of vitamins(B2,B3,B6,and E),medium/long-chain fatty acids(caproic,tetradecanoic,and peptadecanoic acids),and dicarboxylic acids(azelaic and sebacic acids).Our study demonstrated that spraying CPFL significantly could improve piglets’growth performance and immunity,and the beneficial effects are associated with changes in the gut microbiota and host metabolism.Our study has provided novel data for future development of probiotic-based health-promoting strategies and expanded our knowledge of probiotic application in animal husbandry.

Assessment of microbial community structure in human colostrum and mature milk based on geographical location and delivery mode

Breast milk is the most suitable food for the growth and development of infants because it fulfills all the nutritional requirements at this growth stage^([1]).In addition,the wide range of bioactive compounds in milk exerts numerous beneficial effects to infants,including immune system development,protection from infections and metabolism regulation^([2]).

iLABdb:基于WEB的综合乳酸菌数据库

Lactic acid bacteria(LAB)are a group of Gram-positive,facultative anaerobic bacteria that are widely distributed in nature and have important functions in various industrial,medical,and environmental processes[1,2].They are well-known for their ability to produce lactic acid and are thus widely used in the production of fermented foods and beverages,such as yogurt,cheese,and sauerkraut[3].Two of the most prominent and well-studied orders within the LAB group are Lactobacillales and Bifidobacteriales.

自然发酵乳中乳酸菌种内微观多样性及其生态驱动因素

自然发酵乳制品的制作和食用已有数千年历史,其中蕴藏的微生物资源经历了千年的选择与进化,形成了稳定、可遗传的微观生态体系,但是该体系的形成原因和驱动因素尚不清楚.本研究采用培养组学技术和宏基因组学技术对来自5个国家12个地区的12份自然发酵乳制品样本中的乳酸菌微观多样性及其驱动因素进行了系统性的研究.本研究分离并测序了717株代表性的乳酸菌菌株,对自然发酵乳样本进行了深度宏基因组测序,并对其中的214株瑞士乳杆菌、97株乳酸乳球菌乳酸亚种和325株德氏乳杆菌保加利亚亚种进行了系统发育关系的分析.研究发现,同一样本中的乳酸菌菌株具有高度的种内异质性(每个样本平均含有2418~4382个单核苷酸多态性),在进化角度上被分为2~8个进化谱系.绝大多数谱系的碳水化合物和蛋白水解功能具有显著差异.通过对种内特异性基因进行溯源,发现23.93%~53.70%的基因发生水平基因转移事件.此外,样品的微生物组成与各个物种/亚种的核苷酸多样性呈显著负相关关系(r=-0.65,P<0.008).综上所述,本研究发现自然发酵乳种群组成及遗传物质交流是该微观体系的驱动因素,也为自然发酵乳制品的微生物研究提供了生态学见解.

Characteristics of gut microbiota determine effects of specific probiotics strains in patients with functional constipation

To the Editor:Probiotics are a promising treatment modality for functional constipation(FC);however,the factors affecting individual responses to probiotics remain unclear.Growing evidence has identified that there is a strong relationship among the gut microbiota and constipation and related gut-brain axis.[1]The gut microbiota may modulate the gut functions via gut metabolites or trigger the release of gut hormones,such as peptide YY,gastric inhibitory polypeptide,and 5-hydroxytryptamine.[2]In turn,gut hormones affect gut secretion,motility,and sensation through their receptors located on epithelial,enteric,and smooth muscle cells.[2]Based on these findings,exogenous probiotics have been used in patients with constipation;however,few have produced consistent results.[3]In this study,we investigated the efficacy and safety of several specific probiotics strains for constipation,and also examined the potential reasons for the individualized effects of probiotics,which may facilitate interventional decisionmaking for FC patients.

单分子实时测序技术提高了传统发酵乳制品酸马奶中细菌的检测灵敏度

酸马奶是一种传统发酵乳制品,具有丰富的细菌多样性.本研究利用单分子实时测序技术系统分析了酸马奶样品的细菌多样性.结果表明,单分子实时测序技术可以大大提高细菌多样性检测的准确性和灵敏度,特别是低丰度菌群.使用这种方法检测到的物种数量是基于二代测序技术分析方法的3倍左右.有趣的是,除了常见的乳酸菌种类之外,还可检测到乳酸菌稀有物种,例如Lactobacillus parabuchneri、Lactobacillus parakefiri和Leuconostoc citreum,以及其他低丰度非发酵型物种.这项研究拓展了对于酸马奶菌群的认识,同时提出了一种工业生产过程中细菌污染检测的新方法.

Changes in chemical composition,structural and functional microbiome during alfalfa(Medicago sativa)ensilage with Lactobacillus plantarum PS-8

Improving silage production by adding exogenous microorganisms not only maximizes nutrient preservation,but also extends product shelf life.Herein,changes in the quality and quantity of Lactobacillus plantarum PS-8(PS-8)-inoculated alfalfa(Medicago sativa)during silage fermentation were monitored at d 0,7,14,and 28(inoculum dose of PS-8 was 1105 colony forming units[cfu]/g fresh weight;50 kg per bag;10 bags for each time point)by reconstructing metagenomic-assembled genomes(MAG)and Growth Rate InDex(GRiD).Our results showed that the exogenous starter bacterium,PS-8 inoculation,became the most dominating strain by d 7,and possibly played a highly active role throughout the fermentation process.The pH value of the silage decreased greatly,accompanied by the growth of acidproducing microorganisms namely PS-8,which inhibited the growth of harmful microorganisms like molds(4.18 vs.1.42 log cfu/g)and coliforms(4.95 vs.0.66 log most probable number[MPN]/g).The content of neutral detergent fiber(NDF)decreased significantly(41.6%vs.37.6%;dry matter basis).In addition,the abundance and diversity of genes coding microbial carbohydrate-active enzymes(CAZymes)increased significantly and desirably throughout the fermentation,particularly the genes responsible for degrading starch,arabino-xylan,and cellulose.Overall,our results showed that PS-8 was replicating rapidly and consistently during early-and mid-fermentation phases,promoting the growth of beneficial lactic acid bacteria and inhibiting undesirable microbes,ultimately improving the quality of silage.

发酵乳的演进脉络分析

Humans are often curious about why and how early humans had given up raw food in diet?And which came into being first,cooking or fermentation?It was posited,based on the skull and jaw structure,that early hominids spent a lot of time eating food vis-a-vis Homo sapiens.Around 2 million years ago,a significant change occurred,and Homo species started spending less time chewing food,implying that they abandoned eating raw food and started utilizing fire as a tool[1].One possibility could be that they started eating cooked food because it was relatively tender and easy to digest.However,it would require a pot,an oven,or a pit to cook or live near volcanoes.If these were not available then,fermentation could be a robust possibility for this change as it tenders the food,develops fascinating flavor,and stymies putrefaction.