Showing papers by "Catherine Stanton published in 2022"

Impact of antibiotics on the human microbiome and consequences for host health

Abstract: It is well established that the gut microbiota plays an important role in host health and is perturbed by several factors including antibiotics. Antibiotic‐induced changes in microbial composition can have a negative impact on host health including reduced microbial diversity, changes in functional attributes of the microbiota, formation, and selection of antibiotic‐resistant strains making hosts more susceptible to infection with pathogens such as Clostridioides difficile. Antibiotic resistance is a global crisis and the increased use of antibiotics over time warrants investigation into its effects on microbiota and health. In this review, we discuss the adverse effects of antibiotics on the gut microbiota and thus host health, and suggest alternative approaches to antibiotic use.

Fermented Foods, Health and the Gut Microbiome

Abstract: Fermented foods have been a part of human diet for almost 10,000 years, and their level of diversity in the 21st century is substantial. The health benefits of fermented foods have been intensively investigated; identification of bioactive peptides and microbial metabolites in fermented foods that can positively affect human health has consolidated this interest. Each fermented food typically hosts a distinct population of microorganisms. Once ingested, nutrients and microorganisms from fermented foods may survive to interact with the gut microbiome, which can now be resolved at the species and strain level by metagenomics. Transient or long-term colonization of the gut by fermented food strains or impacts of fermented foods on indigenous gut microbes can therefore be determined. This review considers the primary food fermentation pathways and microorganisms involved, the potential health benefits, and the ability of these foodstuffs to impact the gut microbiome once ingested either through compounds produced during the fermentation process or through interactions with microorganisms from the fermented food that are capable of surviving in the gastro-intestinal transit. This review clearly shows that fermented foods can affect the gut microbiome in both the short and long term, and should be considered an important element of the human diet.

Feed your microbes to deal with stress: a psychobiotic diet impacts microbial stability and perceived stress in a healthy adult population

Abstract: The impact of diet on the microbiota composition and the role of diet in supporting optimal mental health have received much attention in the last decade. However, whether whole dietary approaches can exert psychobiotic effects is largely understudied. Thus, we investigated the influence of a psychobiotic diet (high in prebiotic and fermented foods) on the microbial profile and function as well as on mental health outcomes in a healthy human population. Forty-five adults were randomized into either a psychobiotic (n = 24) or control (n = 21) diet for 4 weeks. Fecal microbiota composition and function was characterized using shotgun sequencing. Stress, overall health and diet were assessed using validated questionnaires. Metabolic profiling of plasma, urine and fecal samples was performed. Intervention with a psychobiotic diet resulted in reductions of perceived stress (32% in diet vs. 17% in control group), but not between groups. Similarly, biological marker of stress were not affected. Additionally, higher adherence to the diet resulted in stronger decreases in perceived stress. While the dietary intervention elicited only subtle changes in microbial composition and function, significant changes in the level of 40 specific fecal lipids and urinary tryptophan metabolites were observed. Lastly, microbial volatility was linked to greater changes in perceived stress scores in those on the psychobiotic diet. These results highlight that dietary approaches can be used to reduce perceived stress in a human cohort. Using microbiota-targeted diets to positively modulate gut-brain communication holds possibilities for the reduction of stress and stress-associated disorders, but additional research is warranted to investigate underlying mechanisms, including the role of the microbiota.

A compendium of 32,277 metagenome-assembled genomes and over 80 million genes from the early-life human gut microbiome

Abstract: Age-specific reference genomes of the human gut microbiome can provide higher resolution for metagenomic analyses including taxonomic classification, strain-level genomic investigation and functional characterization. We present the Early-Life Gut Genomes (ELGG) catalog with 32,277 genomes representing 2172 species from 6122 fecal metagenomes collected from children under 3 years old spanning delivery mode, gestational age, feeding pattern, and geography. The ELGG substantially expanded the phylogenetic diversity by 38% over the isolate microbial genomes, and the genomic landscape of the early-life microbiome by increasing recruitment of metagenomic reads to 82.8%. More than 60% of the ELGG species lack an isolate representative. The conspecific genomes of the most abundant species from children differed in gene diversity and functions compared to adults. The ELGG genomes encode over 80 million protein sequences, forming the Early-Life Gut Proteins (ELGP) catalog with over four million protein clusters, 29.5% of which lacked functional annotations. The ELGG and ELGP references provided new insights into the early-life human gut microbiome and will facilitate studies to understand the development and mechanisms of disturbances of the human gut microbiome in early life.

The human milk microbiome aligns with lactation stage and not birth mode

Abstract: We analysed the human milk microbiome in a cohort of 80 lactating women and followed the dynamics in taxa over the course of lactation from birth to 6 months. Two hundred and thirty one milk samples were collected from full-term lactating women at 1, 4, 8 and 24 weeks following birth and analysed for microbiota composition using 16S rRNA sequencing. A significant decrease in milk microbiota diversity was observed throughout the first 6 months of lactation, with the greatest difference seen between week 8 and week 24. Nine genera predominated in milk over lactation from week 1 to week 24, comprising of Staphylococcus, Streptococcus, Pseudomonas, Acinetobacter, Bifidobacterium, Mesorhizobium, Brevundimonas, Flavobacterium, and Rhodococcus; however, fluctuations in these core genera were apparent over time. There was a significant effect of stage of lactation on the microbiome, while no effect of birth mode, infant sex and maternal BMI was observed throughout lactation. Streptococcus had the highest mean relative abundance at week 1 and 24 (17.3% and 24% respectively), whereas Pseudomonas predominated at week 4 (22%) and week 8 (19%). Bifidobacterium and Lactobacillus had the highest mean relative abundance at week 4 (5% and 1.4% respectively), and occurred at a relative abundance of ≤ 1% at all other time points. A decrease in milk microbiota diversity throughout lactation was also observed. This study concluded that lactation stage was the primary driving factor in milk microbiota compositional changes over lactation from birth to 6 months, while mode of delivery was not a factor driving compositional changes throughout human lactation.

The human milk microbiome aligns with lactation stage and not birth mode

Abstract: We analysed the human milk microbiome in a cohort of 80 lactating women and followed the dynamics in taxa over the course of lactation from birth to 6 months. Two hundred and thirty one milk samples were collected from full-term lactating women at 1, 4, 8 and 24 weeks following birth and analysed for microbiota composition using 16S rRNA sequencing. A significant decrease in milk microbiota diversity was observed throughout the first 6 months of lactation, with the greatest difference seen between week 8 and week 24. Nine genera predominated in milk over lactation from week 1 to week 24, comprising of Staphylococcus, Streptococcus, Pseudomonas, Acinetobacter, Bifidobacterium, Mesorhizobium, Brevundimonas, Flavobacterium, and Rhodococcus; however, fluctuations in these core genera were apparent over time. There was a significant effect of stage of lactation on the microbiome, while no effect of birth mode, infant sex and maternal BMI was observed throughout lactation. Streptococcus had the highest mean relative abundance at week 1 and 24 (17.3% and 24% respectively), whereas Pseudomonas predominated at week 4 (22%) and week 8 (19%). Bifidobacterium and Lactobacillus had the highest mean relative abundance at week 4 (5% and 1.4% respectively), and occurred at a relative abundance of ≤ 1% at all other time points. A decrease in milk microbiota diversity throughout lactation was also observed. This study concluded that lactation stage was the primary driving factor in milk microbiota compositional changes over lactation from birth to 6 months, while mode of delivery was not a factor driving compositional changes throughout human lactation.

Critical windows of early-life microbiota disruption on behaviour, neuroimmune function, and neurodevelopment

Abstract: Numerous studies have emphasised the importance of the gut microbiota during early life and its role in modulating neurodevelopment and behaviour. Epidemiological studies have shown that early-life antibiotic exposure can increase an individual's risk of developing immune and metabolic diseases. Moreover, preclinical studies have shown that long-term antibiotic-induced microbial disruption in early life can have enduring effects on physiology, brain function and behaviour. However, these studies have not investigated the impact of targeted antibiotic-induced microbiota depletion during critical developmental windows and how this may be related to neurodevelopmental outcomes. Here, we addressed this gap by administering a broad-spectrum oral antibiotic cocktail (ampicillin, gentamicin, vancomycin, and imipenem) to mice during one of three putative critical windows: the postnatal (PN; P2-9), pre-weaning (PreWean; P12-18), or post-weaning (Wean; P21-27) developmental periods and assessed the effects on physiology and behaviour in later life. Our results demonstrate that targeted microbiota disruption during early life has enduring effects into adolescence on the structure and function of the caecal microbiome, especially for antibiotic exposure during the weaning period. Further, we show that microbial disruption in early life selectively alters circulating immune cells and modifies neurophysiology in adolescence, including altered myelin-related gene expression in the prefrontal cortex and altered microglial morphology in the basolateral amygdala. We also observed sex and time-dependent effects of microbiota depletion on anxiety-related behavioural outcomes in adolescence and adulthood. Antibiotic-induced microbial disruption had limited and subtle effects on social behaviour and did not have any significant effects on depressive-like behaviour, short-term working, or recognition memory. Overall, this study highlights the importance of the gut microbiota during critical windows of development and the subtle but long-term effects that microbiota-targeted perturbations can have on brain physiology and behaviour.

miRNA signatures associated with vulnerability to food addiction in mice and humans

Abstract: Food addiction is characterized by a loss of behavioral control over food intake and is associated with obesity and other eating disorders. The mechanisms underlying this behavioral disorder are largely unknown. We aimed to investigate the changes in miRNA expression promoted by food addiction in animals and humans and their involvement in the mechanisms underlying the behavioral hallmarks of this disorder. We found sharp similitudes between miRNA signatures in the medial prefrontal cortex (mPFC) of our animal cohort and circulating miRNA levels in our human cohort, which allowed us to identify several miRNAs of potential interest in the development of this disorder. Tough decoy (TuD) inhibition of miRNA-29c-3p in the mouse mPFC promoted persistence of the response and enhanced vulnerability to developing food addiction, whereas miRNA-665-3p inhibition promoted compulsion-like behavior and also enhanced food addiction vulnerability. In contrast, we found that miRNA-137-3p inhibition in the mPFC did not lead to the development of food addiction. Therefore, miRNA-29c-3p and miRNA-665-3p could be acting as protective factors with regard to food addiction. We believe the elucidation of these epigenetic mechanisms will lead to advances toward identifying innovative biomarkers and possible future interventions for food addiction and related disorders based on the strategies now available to modify miRNA activity and expression.

First encounters of the microbial kind: perinatal factors direct infant gut microbiome establishment

Abstract: The human gut microbiome harbors a diverse range of microbes that play a fundamental role in the health and well-being of their host. The early-life microbiome has a major influence on human development and long-term health. Perinatal factors such as maternal nutrition, antibiotic use, gestational age and mode of delivery influence the initial colonization, development, and function of the neonatal gut microbiome. The perturbed early-life gut microbiome predisposes infants to diseases in early and later life. Understanding how perinatal factors guide and shape the composition of the early-life microbiome is essential to improving infant health. The following review provides a synopsis of perinatal factors with the most decisive influences on initial microbial colonization of the infant gut.

Decreased Tissue Omega-6/Omega-3 Fatty Acid Ratio Prevents Chemotherapy-Induced Gastrointestinal Toxicity Associated with Alterations of Gut Microbiome

Abstract: Gastrointestinal toxicity (GIT) is a debilitating side effect of Irinotecan (CPT-11) and limits its clinical utility. Gut dysbiosis has been shown to mediate this side effect of CPT-11 by increasing gut bacterial β-glucuronidase (GUSB) activity and impairing the intestinal mucosal barrier (IMB). We have recently shown the opposing effects of omega-6 (n-6) and omega-3 (n-3) polyunsaturated fatty acids (PUFA) on the gut microbiome. We hypothesized that elevated levels of tissue n-3 PUFA with a decreased n-6/n-3 PUFA ratio would reduce CPT-11-induced GIT and associated changes in the gut microbiome. Using a unique transgenic mouse (FAT-1) model combined with dietary supplementation experiments, we demonstrate that an elevated tissue n-3 PUFA status with a decreased n-6/n-3 PUFA ratio significantly reduces CPT-11-induced weight loss, bloody diarrhea, gut pathological changes, and mortality. Gut microbiome analysis by 16S rRNA gene sequencing and QIIME2 revealed that improvements in GIT were associated with the reduction in the CPT-11-induced increase in both GUSB-producing bacteria (e.g., Enterobacteriaceae) and GUSB enzyme activity, decrease in IMB-maintaining bacteria (e.g., Bifidobacterium), IMB dysfunction and systemic endotoxemia. These results uncover a host–microbiome interaction approach to the management of drug-induced gut toxicity. The prevention of CPT-11-induced gut microbiome changes by decreasing the tissue n-6/n-3 PUFA ratio could be a novel strategy to prevent chemotherapy-induced GIT.

Dynamic Changes in the Human Milk Metabolome Over 25 Weeks of Lactation

Abstract: Human milk (HM) provides essential nutrition for ensuring optimal infant growth and development postpartum. Metabolomics offers insight into the dynamic composition of HM. Studies have reported the impact of lactation stage, maternal genotype, and gestational age on HM metabolome. However, the majority of the studies have considered changes within the first month of lactation or sampled with large intervals. This leaves a gap in the knowledge of progressing variation in HM composition beyond the first month of lactation. The objective of this study was to investigate whether the HM metabolome from mothers with term deliveries varies beyond 1 month of lactation, during the period in which HM is considered fully mature. Human milk samples (n = 101) from 59 mothers were collected at weeks 1–2, 3–5, 7–9, and 20–25 postpartum and analyzed using 1H nuclear magnetic resonance spectroscopy. Several metabolites varied over lactation and exhibited dynamic changes between multiple time points. Higher levels of HM oligosaccharides, cis-aconitate, O-phosphocholine, O-acetylcarnitine, gluconate, and citric acid were observed in early lactation, whereas later in lactation, levels of lactose, 3-fucosyllactose, glutamine, glutamate, and short- and medium-chain fatty acids were increased. Notably, we demonstrate that the HM metabolome is dynamic during the period of maturity.

Sex, pain, and the microbiome: The relationship between baseline gut microbiota composition, gender and somatic pain in healthy individuals

Abstract: Relative to men, women present with pain conditions more commonly. Although consistent differences exist between men and women in terms of physiological pain sensitivity, the underlying mechanisms are incompletely understood and yet could inform the development of effective sex specific treatments for pain. The gut microbiota can modulate nervous system functioning, including pain signaling pathways. We hypothesized that the gut microbiota and critical components of the gut-brain axis might influence electrical pain thresholds. Further, we hypothesized that sex, menstrual cycle, and hormonal contraceptive use might account for inter-sex differences in pain perception.Healthy, non-obese males (N = 15) and females (N = 16), (nine of whom were using hormonal contraceptives), were recruited. Male subjects were invited to undergo testing once, whereas females were invited three times across the menstrual cycle, based on self-reported early follicular (EF), late follicular (LF), or mid-luteal (ML) phase. On test days, electrical stimulation on the right ankle was performed; salivary cortisol levels were measured in the morning; levels of lipopolysaccharide-binding protein (LBP), soluble CD14 (sCD14), pro-inflammatory cytokines were assessed in plasma, and microbiota composition and short-chain fatty acids (SCFAs) levels were determined in fecal samples.We observed that the pain tolerance threshold/pain sensation threshold (PTT/PST) ratio was significantly lesser in women than men, but not PST or PTT alone. Further, hormonal contraceptive use was associated with increased LBP levels (LF & ML phase), whilst sCD14 levels or inflammatory cytokines were not affected. Interestingly, in women, hormonal contraceptive use was associated with an increase in the relative abundance of Erysipelatoclostridium, and the relative abundances of certain bacterial genera correlated positively with pain sensation thresholds (Prevotella and Megasphera) during the LF phase and cortisol awakening response (Anaerofustis) during the ML phase. In comparison with men, women displayed overall stronger associations between i) SCFAs data, ii) cortisol data, iii) inflammatory cytokines and PTT and PST.Our findings support the hypothesis that the gut microbiota may be one of the factors determining the physiological inter-sex differences in pain perception. Further research is needed to investigate the molecular mechanisms by which specific sex hormones and gut microbes modulate pain signaling pathways, but this study highlights the possibilities for innovative individual targeted therapies for pain management.

Effect of diet on pathogen performance in the microbiome

Abstract: Intricate interactions among commensal bacteria, dietary substrates and immune responses are central to defining microbiome community composition, which plays a key role in preventing enteric pathogen infection, a dynamic phenomenon referred to as colonisation resistance. However, the impact of diet on sculpting microbiota membership, and ultimately colonisation resistance has been overlooked. Furthermore, pathogens have evolved strategies to evade colonisation resistance and outcompete commensal microbiota by using unique nutrient utilisation pathways, by exploiting microbial metabolites as nutrient sources or by environmental cues to induce virulence gene expression. In this review, we will discuss the interplay between diet, microbiota and their associated metabolites, and how these can contribute to or preclude pathogen survival.

Metabolomic Workflow for the Accurate and High-Throughput Exploration of the Pathways of Tryptophan, Tyrosine, Phenylalanine, and Branched-Chain Amino Acids in Human Biofluids

Abstract: The modulation of host and dietary metabolites by gut microbiota (GM) is important for maintaining correct host physiology and in the onset of various pathologies. An ultrahigh-performance liquid chromatography-electrospray ionization-tandem mass spectrometry method was developed for the targeted quantitation in human plasma, serum, and urine of 89 metabolites resulting from human-GM cometabolism of dietary essential amino acids tryptophan, tyrosine, and phenylalanine as well as branched-chain amino acids. Ninety-six-well plate hybrid-SPE enables fast clean-up of plasma and serum. Urine was diluted and filtered. A 15 min cycle enabled the acquisition of 96 samples per day, with most of the metabolites stable in aqueous solution for up to 72 h. Calibration curves were specifically optimized to cover expected concentrations in biological fluids, and limits of detection were at the order of ppb. Matrix effects were in acceptable ranges, and analytical recoveries were in general greater than 80%. Inter and intraday precision and accuracy were satisfactory. We demonstrated its application in plasma and urine samples obtained from the same individual in the frame of an interventional study, allowing the quantitation of 51 metabolites. The method could be considered the reference for deciphering changes in human-gut microbial cometabolism in health and disease. Data are available via Metabolights with the identifier MTBLS4399.

Different Effects of Different Lactobacillus acidophilus Strains on DSS-Induced Colitis

Abstract: Inflammatory bowel disease (IBD) is a worldwide chronic intestinal inflammatory immune-related disease. In this study, mice with dextran sulfate sodium (DSS)-induced colitis were used to evaluate the effect of Lactobacillus acidophilus on colitis. The results revealed that L. acidophilus CCFM137 and FAHWH11L56 show potential for relieving colitis symptoms, while L. acidophilus FGSYC48L79 did not show a protective effect. Moreover, L. acidophilus NCFM and FAHWH11L56 showed similar effects on various indicators of DSS-induced colitis, increasing the IL-10 and IL-17 in the colon, and modifying the CCL2/CCR2 axis and CCL3/CCR1 axis. For L. acidophilus CCFM137, its effects on colitis were different from the above two strains. Moreover, L. acidophilus FGSYC48L79 had negative effects on colitis by increasing the abundance of harmful bacteria in the gut microbiota and may promote the signaling of chemokines and their receptors. This may be related to its special genome compared to the other strains.

A systematic review of breast milk microbiota composition and the evidence for transfer to and colonisation of the infant gut.

Abstract: The intestinal microbiota plays a major role in infant health and development. However, the role of the breastmilk microbiota in infant gut colonisation remains unclear. A systematic review was performed to evaluate the composition of the breastmilk microbiota and evidence for transfer to/colonisation of the infant gut. Searches were performed using PUBMED, OVID, LILACS and PROQUEST from inception until 18th March 2020 with a PUBMED update to December 2021. 88 full texts were evaluated before final critique based on study power, sample contamination avoidance, storage, purification process, DNA extraction/analysis, and consideration of maternal health and other potential confounders. Risk of skin contamination was reduced mainly by breast cleaning and rejecting the first milk drops. Sample storage, DNA extraction and bioinformatics varied. Several studies stored samples under conditions that may selectively impact bacterial DNA preservation, others used preculture reducing reliability. Only 15 studies, with acceptable sample size, handling, extraction, and bacterial analysis, considered transfer of bacteria to the infant. Three reported bacterial transfer from infant to breastmilk. Despite consistent evidence for the breastmilk microbiota, and recent studies using improved methods to investigate factors affecting its composition, few studies adequately considered transfer to the infant gut providing very little evidence for effective impact on gut colonisation.

Gut microbiota insights into human adaption to high-plateau diet.

Abstract: Modern genome analyses have identified unique genetic variations of indigenous people in terms of human adaptation to the low-oxygen condition in high plateaus [6]. On the other hand, other key aspects such as diet have been an important consideration for human adaptation to such high-plateau environments [2]. In ancient times, indigenous nomads often lack vegetables and fruits because of geographic limitations causing difficulties in trading agricultural products with low-altitude people, for example, Tea-Horse Road was an important but time-consuming trade path in the past for Tibetans to obtain the dark tea from low-altitude tea manufacturers. Through long-term dietary self-selection, dark tea becomes an essential part of nomadic diets in high plateaus and low-altitude steppe areas (Figure 1A). Of note, consumption of fermented milk products is a tradition for thousands of years in nomadic diets (Figure 1A). Both tea and fermented milk are widely recognized to contain functional ingredients to confer health-promoting benefits to humans, but further confirmation in nomadic populations is merited. Even after the advancement of transportation and food globalization, modern high-altitude minorities usually maintain their nomadic dietary habits. From the standpoint of modern nutrition, nomadic diet is a minimally processed diet with low contents of vegetables and fruits and should not be regarded as a balanced diet, but it is quite distinct from the Western diet, a modern diet that contains high amounts of processed and prepackaged foods, red meat, and high-fat and high-sugar foods. Prior efforts have demonstrated the importance of host–diet–gut microbiota interactions in human health for a low-altitude population with the Western diet. Thus, there is a need to dissect the interaction between nomadic diet and gut microbiota of high-plateau minorities, and gut microbiota research might shed new light on human adaption to the high-plateau environment linking to nomadic diet. We performed a meta-analysis of more than 1000 previously published shotgun metagenomes of adult people from nomadic regions of Tibetan and Mongolian Plateaus and Kazakh Steppe, and low-altitude people from Europe, the United States, and China. To minimize the batch effect across different data sets, we did not perform assembly-based metagenomic analysis that requires high sequencing depths, rather we applied marker gene-based operational taxonomic units (mOTUs; version 2.6) that use 10 universal single-copy marker genes for taxonomic profiling with high precision and low error [3]. Compared to the low-altitude population, people from nomadic regions have distinct gut microbiota composition (Figure 1B), which is largely dominated by Prevotella (Figure 1C). While it is well known that industrial diet is responsible for the formation of Bacteroides enterotype in people receiving Western diet, it is surprising that many people commonly harbor Prevotella enterotype independent of nomadic regions (Figure 1C,D), which could be induced by high intake of cereal products in their diets [4]. More interestingly, enterotype analysis indicated that Tibetans from Yunnan (PRJNA588513) having a higher intake of diverse vegetables and fruits are different from Tibetans from Tibet (PRJNA543906) with traditional nomadic diet (Figure 1D). This suggests that dietary alteration could shift gut enterotype significantly. There have been several important studies demonstrating Prevotella is associated with exacerbation of autoimmune diseases, such as rheumatoid arthritis [5-8]. It is highly speculative that the high prevalence of rheumatoid arthritis [9, 10] in the Tibetan population could be associated with their common gut Prevotella enterotype, thus further studies are required to validate such causation and to investigate whether the dietary intervention could be a potential strategy to effectively prevent the occurrence of rheumatoid arthritis. Of note, tea [11] and fermented milk [12] have been shown to lower host systematic inflammation though they could have limited alterations to gut microbiota composition. It is quite interesting to see the frequent consumption of tea and fermented milk in Tibetan, Mongolian, and Kazakh populations (Figure 1A), but linking such dietary habits to reduced inflammation is questionable and requires a systematic design of diet intervention to confirm it. Interestingly, we observed a significantly (p < 0.05; Wilcoxon test) higher alpha-diversity in people with Prevotella enterotype in nomadic regions than that in low-altitude people of the same enterotype (Figure 1D). While it is not clear whether such higher microbial diversity could be helpful against Prevotella-associated inflammation, it is likely to play a role in host health since the loss of microbial diversity is associated with several human conditions [13]. In addition, as shown in Figure 1E, we found that gut enterotype was largely unaltered during the seasonal shift in one Kazakh data set (PRJEB17632) because nomadic dietary habits could be commonly excised by modern Kazakh. This is a quite different observation from a prior report on seasonal variations in gut microbiota composition in the Hadza hunter–gatherers of Tanzania [14]. Taken together, a distinct gut Prevotella enterotype of high microbial diversity is highly prevalent in people from nomadic regions. Our preliminary evidence from population-scale gut microbiota meta-analysis is encouraging, but future research efforts are necessary to understand human adaptation to nomadic diet with insights into host–diet–gut microbiota interactions. Most likely, long-term high cereal consumption could explain the dominance of Prevotella enterotype in people of nomadic regions where carbohydrate-based diet is more affordable in addition to its sufficient energy and biofunctionalities [4, 15]. For example, highland barley is rich in beta-glucan and its high molecular weight form has been clinically shown to reduce blood cholesterol levels via the enhanced bile acids synthesis in the liver and the increased fecal excretion of secondary bile acids [16]. Low levels of blood cholesterol inhibit the formation of plaques in the blood vessels, which indirectly favors the control of blood pressure that is the top risk factor driving the most death and disability in nomadic regions, thus the high intake of barely products in the Tibetan population seems to be beneficial for host health. However, whether a Prevotella enterotype of high microbial diversity is responsible for the increased biotransformation of secondary bile acids is of great interest but remains largely unknown. Additionally, a high-fat diet has been shown to reduce Prevotella abundance [15, 17]; we noticed this conflicting observation typically in Prevotella-dominated Tibetan because they consume Yak butter tea and barely-based food on a daily basis. Butter tea is an emulsified beverage through physical processing, so it is not clear whether fat absorption is prohibited by emulsification or by tea ingredients, that is, tea polyphenols and their derivatives. Importantly, Prevotella enterotype is associated with the host genotype of rheumatoid arthritis before disease onset [6, 7], enhances disease susceptibility, and exacerbates disease severity of rheumatoid arthritis and colonic inflammation [5, 8]. Because rheumatoid arthritis is the second highly prevalent (8%) chronic disease in Tibet [10], it becomes important to understand how the host responds to proinflammatory Prevotella enterotype in the gut and what components in nomadic diet could reverse such inflammation status. For example, tea ingredients have been documented as anti-inflammatory agents, whereas a recent human dietary intervention study for low-altitude individuals of Bacteroides enterotype reported that consumption of fermented foods increased gut microbial diversity and decreased inflammatory markers [12], but whether such health-promoting benefits could be recapitulated in individuals of Prevotella enterotype remains to be elucidated. Overall, nomadic diet is likely associated with Prevotella expansion and is associated with several major chronic diseases in people of nomadic regions but requires further systematic assessment on host–diet–gut microbiota interactions. It is necessary to understand the pros and cons of traditional nomadic diets in terms of host health before establishing new nutritional guidelines for people of nomadic regions. Despite technical and analytic advancements of gut microbiota research for the past decade, there have been several challenges in conducting gut microbiota research for high-plateau populations. Thus, we highlight those challenges and discuss corresponding strategies to tackle them. First, infrastructure advancement and food globalization have significant impacts on the accessibility of food resources, including fresh vegetables and fruits, which ultimately change gut microbiota composition as evidenced by two Tibetan data sets (Yunnan and Tibet; Figure 1D) that we included in our meta-analysis. At the current stage, higher food accessibility shifts their dietary pattern thus limiting the eligibility and the size of subjects maintaining traditional nomadic diets to be recruited for gut microbiota research, especially if disease prevalence and pathogenesis are the major focus of host–diet–gut microbiota association study. To avoid the effects of nonnomadic foods, longitudinal, randomized cross-over diet intervention with nomadic and nonnomadic foods could be considered, but the duration of each intervention should be carefully considered. If necessary, a cross-over trial could be repeated immediately after the first trial to gain more insights and might be useful to assess the stability of gut microbiota and the effect of seasonal cycling. Second, the size of nomadic regions, including Tibetan and Mongolian Plateaus and Kazakh Steppe, is over 10 million square meters, and traditional nomads remain unsettled making gut microbiota research extremely difficult; that is, clinical visits, follow-up, and longitudinal sampling are of major concerns. Appropriate stool shipping is another concern because preserving microbial composition and bioactivity is important for further DNA/RNA extraction, sequencing, and microbial isolation. A virtual clinical visit could be highly helpful because telecommunications are now largely covered for high plateaus, thus this approach seems to be useful for people with a nomadic lifestyle. To tackle the sampling challenge, there could be two potential solutions to include stool collection during: (1) large disease screenings. For example, screening of hydatidosis, a major zoonosis of parasitic infection in Tibet, has been performed for more than three million Tibetan people from 2016 to 2017 and (2) national health service surveys. Those surveys of high administrative level are held regularly and are suitable for such purpose, but require study permission and detailed administrative coordination. Those governmental mission-orientated screenings and surveys are highly recommended because additional clinical metadata could be collected for disease-microbiota associations with consideration of geographic influence, human development (particularly children and elderly), gender difference, dietary information, and so forth. For example, the prevalence of rheumatoid arthritis is more common in the elderly compared with the younger population in Tibet, thus requiring an age-stratified analysis. Finally, gut microbiota profiling and bacterial isolation are big challenges. Because targeted (16S ribosomal RNA [rRNA] and Internal Transcribed Spacer [ITS]) metagenomic analysis is not appropriate for precision compositional and functional profiling, a shotgun metagenomic analysis should be considered for such profiling. However, there is a large proportion of uncultured bacteria, including Clostridiales Family Incertae Sedis and Firmicutes Family Incertae Sedis, in the high-plateau population. Since gut microbiota composition of the high-plateau population is very unique compared to low-altitude people, the computational effort is required to construct MAGs from shotgun metagenomes of the high-plateau population. However, MAGs are consensus sequences constructed from the phylogenetic closely related strains or species of high identity and the genome completion of MAGs is usually not comparable to single genomes of cultivable microbes thus limiting further strain-level and genome-scale characterization. Future studies also need to focus on the isolation of gut commensal microbes from high-plateau people, and preserving live gut anaerobic microbes during sample collection and shipping is essential for such a task. Since metabolic reconstruction for MAGs could potentially predict the essential nutrients for microbial growth, the computational effort might help the design of a culture medium for targeted isolation. Taken together, high-plateau people have an identical gut microbiota of Prevotella enterotype, and such proinflammatory enterotype is generally thought to be associated with nomadic diet patterns. Several characteristic food ingredients, including tea and fermented foods, in nomadic diet, have been shown to be helpful to tackle Prevotella-centered chronic diseases but require a further comprehensive assessment of host–diet–gut microbiota interactions. However, gut microbiota research for people of high-plateau regions needs to consider several unneglectable challenges, and such effort is to advance current nutritional guidelines and dietary interventions for promoting their health status. This study is supported by the National Institute of Allergy and Infectious Diseases (P01-AI152999 and U01-AI124290). The authors declare that there are no conflict of interests. Qinglong Wu and Mingfu Wang conceived the idea. Yina Huang, Jinxin Liu, and Qinglong Wu collected data and performed analysis. Hein Min Tun, Catherine Stanton, Tingtao Chen, Hani El-Nezami, and Hua Wei interpreted and discussed results. All authors contributed to the writing of the manuscript. Shotgun metagenomic data used in this meta-analysis are available from the NCBI Sequence Read Archive database with accession numbers indicated in this paper. The figures related tables and scripts were deposited in https://github.com/qinglong89/Nomad-Prevotella.

Emulsion-Based Postbiotic Formulation Is Comparable to Viable Cells in Eliciting a Localized Immune Response in Dairy Cows With Chronic Mastitis

Abstract: Bovine mastitis is a disease with a multi-etiological nature, defined as an infection and inflammation of the udder. Mastitis represents a significant ongoing concern in the dairy industry, leading to substantial losses in profits and revenue for farmers worldwide. The predominant causes of bovine mastitis include the pathogens Staphylococcus aureus, Streptococcus dysgalactiae, Streptococcus uberis, and Escherichia coli. Antibiotic administration is currently the main treatment option for mastitis. However, there is a pressing need for alternative therapies to treat and prevent the disease, especially with the emergence of antibiotic-resistant, mastitis-causing pathogens, resulting in antibiotic treatment failure. One such example is live bio-therapeutics (also known as probiotics), such as Lactococcus lactis DPC3147. The efficacy of this live bio-therapeutic has been demonstrated in several previous trials by our group. The most recent of these trials showed that an emulsion-based formulation of this strain was as effective as a commercial antibiotic formulation in treating sub-clinical and clinical cases of bovine mastitis. Here, we report the results of a follow-up field trial, in which we sought to gain insight into the mechanism of action of such live bio-therapeutics, focussing on chronic mastitis cases. We treated 28 cows with chronic mastitis with two separate emulsion-based formulations containing either viable L. lactis DPC3147 cells (15 cows) or heat-killed L. lactis DPC3147 cells (13 cows). We then evaluated the efficacies of the two formulations (two treatment groups) in terms of stimulating a localized immune response (quantified by measuring IL-8 concentrations in milk collected from udders affected by mastitis) and efficacies in terms of cure rates (quantified by reductions in somatic cell counts and absence of pathogens). We demonstrate that the presence of heat-inactivated bacteria (a postbiotic) was as effective as the live bio-therapeutic in eliciting a localized immune response in cows with chronic mastitis. The response to heat-killed cells (postbiotic) reported herein could have beneficial implications for farmers with regard to prolonging the shelf life of such emulsion-based formulations containing heat-killed cells of L. lactis DPC3147 for curing cows with mastitis.

Lactation time influences the composition of Bifidobacterium and Lactobacillus at species level in human breast milk.

Abstract: Human breast milk is a source of microorganisms for infants that play an important role in building infant gut health and immunity. The bacterial composition in human breast milk is influenced by lactation time. This study aimed to investigate the influence of lactation time on bacteria in breast milk at the genus level and the species levels of Bifidobacterium and Lactobacillus on days 2-4, 8, 14, and 30. Eighteen individuals were recruited and 60 milk samples were collected. The 16S rRNA gene, and the bifidobacterial groEL and lactobacilli groEL genes were used for amplicon sequencing. The results revealed that the alpha diversities of colostrum and transition 1 (day 8) milk were lower than that of transition 2 (day 14) and mature milk. PCoA analysis showed that bacterial composition in colostrum and transition 1 milk differed from transition 2 and mature milk. A lower relative abundance of Blautia was found in colostrum and transition 1 milk compared with mature milk and lower abundances of Ruminococcus, Dorea, and Escherichia-Shigella were found in transition 1 compared with mature milk. Bifidobacterium ruminantium, Limosilactobacillus mucosae, and Ligilactobacillus ruminis were the predominant species across all four lactation stages, while Bifidobacterium bifidum was lower in transition 1, and Bifidobacterium pseudocatenulatum and Bifidobacterium pseudolongum were higher in transition 1 milk. This study indicated that the bacterial composition in colostrum was more similar to that of transition 1 milk, whereas the bacterial community in transition 2 milk was similar to that of mature milk which suggests that bacterial composition in human breast milk shows stage-specific signatures even within a short period at both genus level and Bifidobacterium and Lactobacillus species levels, providing insights into probiotic supplementation for the nursing mother.

Exploiting lactic acid bacteria for colorectal cancer: a recent update.

Abstract: Colorectal cancer (CRC) is the third most common cancer in the world. Currently, chemotherapy and radiotherapy used to treat CRC exhibit many side effects, hence, it is an urgent need to design effective therapies to prevent and treat CRC. Lactic acid bacteria (LAB) can regulate gut microbiota, intestinal immunity, and intestinal mechanical barrier, which is becoming a hot product for the prevention and treatment of CRC, whereas comprehensive reviews of their anti-CRC mechanisms are limited. This review systematically reveals the latest incidence, mortality, risk factors, and molecular mechanisms of CRC, then summarizes the roles of probiotics in alleviating CRC in animal and clinical studies and critically reviews the possible mechanisms by which these interventions exert their activities. It then shows the limitations in mechanisms and clinical studies, and the suggestions for future research are also put forward, which will play an important role in guiding and promoting the basic and clinical research of remising CRC by LAB and the development of LAB products.

Characterization of CRISPR-Cas systems in Bifidobacterium breve

Abstract: The clustered regularly interspaced short palindromic repeat (CRISPR)-CRISPR-associated protein (Cas) system is an important adaptive immune system for bacteria to resist foreign DNA infection, which has been widely used in genotyping and gene editing. To provide a theoretical basis for the application of the CRISPR-Cas system in Bifidobacterium breve , the occurrence and diversity of CRISPR-Cas systems were analysed in 150 B. breve strains. Specifically, 47 % (71/150) of B. breve genomes possessed the CRISPR-Cas system, and type I-C CRISPR-Cas system was the most widely distributed among those strains. The spacer sequences present in B. breve can be used as a genotyping marker. Additionally, the phage assembly-related proteins were important targets of the type I-C CRISPR-Cas system in B. breve , and the protospacer adjacent motif sequences were further characterized in B. breve type I-C system as 5′-TTC-3′. All these results might provide a molecular basis for the development of endogenous genome editing tools in B. breve .

The microbiome modulating potential of superheated steam (SHS) treatment of dietary fibres

Abstract: In this study, wheat and oat bran fibres were used to investigate the potential beneficial prebiotic-enhancing effects of superheated steam (SHS) treatment. Following SHS treatment of fibres, in-vitro simulated gastric and intestinal digestion followed by batch culture fermentation was performed. 16S rRNA gene sequencing and short chain fatty acid analysis were conducted, which demonstrated that SHS treatment was associated with significant differences in beta diversity and the relative abundances of several microbial taxa. Principal Coordinate Analysis (PCoA) revealed significant separation between SHS-treated oat and non-treated oat (p = 0.013), and between SHS-treated wheat and non-treated wheat following in vitro batch fermentation (p = 0.042). Abundances of Ruminococcus were found to be significantly higher by 1.09-log in SHS-treated oat when compared with non-treated oat while abundances of Escherichia_Shigella, and Alistipes were significantly lower by 1.47-log and 0.39-log, respectively in the SHS-treated oat samples than the non-treated oat samples (p = 6.85E-06, p = 0.002037, p = 0.002458; respectively). These data demonstrate that SHS treatment of dietary fibre enhanced its effectiveness to modulate the gut microbiome. Industrial Relevance: Superheated steam (SHS) treatment has emerged as an effective method to improve the shelf-life of grains by reducing lipid hydrolysis and oxidation. Our results revealed that SHS treatment of wheat and oat brans led to increased physiological and chemical properties including higher water-binding capacity, water-extractable arabinoxylan, and total phenolics as well as improvement in human gut microbiota. Our results suggest that this method could be implemented in the food industry in order to improve beneficial properties of oat and wheat brans.

Effects of Bifidobacterium with the Ability of 2′-Fucosyllactose Utilization on Intestinal Microecology of Mice

Abstract: In breast milk, 2′-Fucosyllactose (2′FL) is the most abundant breast milk oligosaccharide and can selectively promote the proliferation of bifidobacteria. This study aimed to explore the effect of ifidobacterial with different utilization capacities of 2′FL on the intestinal microecology of mice. Furthermore, the effects of ifidobacterial with different 2′FL utilization capabilities on mice gut microbiota under the competitive pressure of 2′FL as a carbon source were explored. Compared with the control group, 2′FL, Bifidobacterium (B.) bifidum M130R01M51 + 2′FL, B. longum subsp. Longum CCFM752, and CCFM752 + 2′FL treatments significantly decreased the food intake. Moreover, the water intake, body weight, and fecal water content in all groups showed no significant difference compared with the control group. The combination of B. longum subsp. longum CCFM752 and 2′FL can significantly increase the levels of pro-inflammatory and anti-inflammatory factors. B. bifidum M130R01M51 and mixed strains combined with 2′FL significantly increased the contents of acetic acid and isobutyric acid. The results showed that B. bifidum M130R01M51, B. breve FHuNCS6M1, B. longum subsp. longum CCFM752, and B. longum subsp. infantis SDZC2M4 combined with 2′FL significantly increased the species richness of the gut microbiota. Moreover, B. longum subsp. longum CCFM752 and B. longum subsp. infantis SDZC2M4 significantly increased the abundance of Faecalibaculum and Bifidobacterium, respectively. In conclusion, exploring the impact on intestinal microecology can provide theoretical guidance for the development of personalized prebiotics for different bifidobacteria, which has the potential to improve the ecological imbalance of infant gut microbiota.

Cross-sectional observational study protocol: missing microbes in infants born by caesarean section (MiMIC): antenatal antibiotics and mode of delivery

Abstract: Introduction The intestinal microbiome in early life plays a major role in infant health and development. Factors like antibiotic exposure, breast/formula feeding and mode of delivery are known to affect the microbiome. The increasing occurrence of caesarean section (C-section) deliveries and antibiotic exposure warrants further insight into the potential missing microbes in those infants. The study objective is to study the effect of maternal antibiotic administration during pregnancy and/or C-section mode of delivery on the development of the infant’s intestinal microbiome until the age of 2 years. Methods and analysis A single site, cross-sectional observational study of C-section and vaginally delivered infants being either exposed to maternal antibiotic treatment or not during the third trimester of pregnancy. Throughout the nine visits, stool, urine, saliva, hair, breast milk and vaginal swabs will be collected from either mother and/or infant for microbiome and metabolomic analysis. Ethics and dissemination The protocol was approved by the Clinical Research Ethics Committee of the Cork Teaching Hospitals. The trial has been registered at ClinicalTrials.gov. The findings from this study will be disseminated in peer-reviewed journals, during scientific conferences, and directly to the study participants. Sequencing data will be deposited in public databases. Trial registration number NCT04134819.

Shared and Non-Shared sIgA-Coated and -Uncoated Bacteria in Intestine of Mother–Infant Pairs

Abstract: The infant gut microbiota is critical for promoting and maintaining early-life health. The study aimed to analyze the composition of sIgA-coated and sIgA-uncoated bacterial communities at genus level and lactobacilli and bifidobacterial communities at species level in human breast milk (HBM) and infant and maternal feces. Eleven pregnant women were recruited successfully. HBM; infant feces during colostrum, transition, and mature stages; and maternal feces within the mature stage were collected. sIgA-coated and sIgA-uncoated bacteria were separated with magnetic-activated cell sorting. Then, 16S rRNA sequencing, bifidobacterial groEL gene sequencing, and lactobacilli groEL gene sequencing were performed to analyze the bacterial community. PCoA revealed that the compositions of sIgA-coated and sIgA-uncoated bacteria were different among HBM and infant and maternal feces. Higher relative abundance of sIgA-uncoated Bifidobacterium was found in the three lactation stages in infant feces compared to the corresponding HBM, and a higher relative abundance of sIgA-uncoated Faecalibacterium was found in maternal feces compared to HBM and infant feces. For bifidobacterial community, sIgA-coated and sIgA-uncoated B. longum subsp. infantis and B. pseudocatenulatum was dominant in infant feces and maternal feces, respectively. The relative abundance of sIgA-uncoated B. longum subsp. infantis was significantly higher in infant feces compared to that in maternal feces. For the Lactobacillus community, L. paragasseri and L. mucosae were dominant in infant and maternal feces, respectively. HBM and infant and maternal feces showed distinct diversity and composition of both sIgA-coated and sIgA-uncoated bacteria at genus level. Infant and maternal feces showed similar composition of Bifidobacterium at species level. The same Bifidobacterium species could be detected both in sIgA-coated and -uncoated form. This article provided deeper understanding on the microbiota profile in HBM and infant and maternal feces.