The human gut microbiome is typically characterized from stool samples, yet microbial communities vary across intestinal regions and microenvironments. Here, we performed spatially resolved deep whole-genome shotgun sequencing of paired luminal and mucosal samples collected across six intestinal segments from organ donors to characterize the organization of bacterial, archaeal, fungal, viral, and resistome components within the human intestine. Distinct microbial domains exhibited different spatial organization patterns: bacterial communities showed moderate longitudinal partitioning, methanogenic archaea displayed strong distal enrichment and mucosal association, viral distributions largely mirrored predicted bacterial hosts, and fungal communities showed comparatively weak spatial structure and strong donor dependence. Mucosa-associated communities showed a trend toward enrichment in enzymatic functions associated with host substrates. In contrast, resistome profiles were shaped predominantly by donor identity rather than anatomical location, highlighting the individualized nature of antimicrobial resistance reservoirs. Spatially distinct microbial association structures suggested niche-dependent ecological organization. Together, these findings support a model of the human intestine as a spatially structured, individualized microbial ecosystem and highlight the limitations of stool as a universal proxy for gut microbiome organization.

INTRODUCTION:Common oral diseases are known to be associated with dysbiotic shifts in the supragingival microbiome, yet most oral microbiome associations with clinical end points emanate from cross-sectional studies. Orthodontic treatment is an elective procedure that can be exploited to prospectively examine clinically relevant longitudinal changes in the composition and function of the supragingival microbiome.METHODS:A longitudinal cohort study was conducted among 24 adolescent orthodontic patients who underwent saliva and plaque sampling and clinical examinations at time points: before fixed appliance bonding and at 1, 6, and 12 wk thereafter. Clinical indices included bleeding on probing (BOP), mean gingival index (GI), probing depths (PDs), and plaque index (PI). To study the biologically (i.e., transcriptionally) active microbial communities, RNA was extracted from plaque and saliva for RNA sequencing and microbiome bioinformatics analysis. Longitudinal changes in microbiome beta diversity were examined using PERMANOVA tests, and the relative abundance of microbial taxa was measured using Kruskal-Wallis tests, Wilcoxon rank-sum tests, and negative binomial and zero-inflated mixed models.RESULTS:Clinical measures of oral health deteriorated over time-the proportion of sites with GI and PI ≥1 increased by over 70% between prebonding and 12 wk postbonding while the proportion of sites with PD ≥4 mm increased 2.5-fold. Streptococcus sanguinis, a health-associated species that antagonizes cariogenic pathogens, showed a lasting decrease in relative abundance during orthodontic treatment. Contrarily, caries- and periodontal disease-associated taxa, including Selenomonas sputigena, Leptotrichia wadei, and Lachnoanaerobaculum saburreum, increased in abundance after bonding. Relative abundances of Stomatobaculum longum and Mogibacterium diversum in prebonding saliva predicted elevated BOP 12 wk postbonding, whereas Neisseria subflava was associated with lower BOP.CONCLUSIONS:This study offers insights into longitudinal community and species-specific changes in the supragingival microbiome transcriptome during fixed orthodontic treatment, advancing our understanding of microbial dysbioses and identifying targets of future health-promoting clinical investigations.KNOWLEDGE TRANSFER STATEMENT:Bonding braces was associated with subsequent changes in the oral microbiome characterized by increases in disease-associated species, decreases in health-associated species, and worsened clinical measures of oral health.

[This corrects the article DOI: 10.3389/frmbi.2022.1041752.].

Little is known regarding the impact of diet on the breast milk microbiome. We hypothesized that vegan, vegetarian, and omnivore diets would impact the human milk microbiota. We also aimed to explore associations between human milk fatty acid concentrations and microbial composition. A cross-sectional microbiome diversity analysis of human milk samples (N = 72) was performed using 16S rRNA amplicon sequencing. Human milk microbial diversity was not associated with diet type. However, analysis of microbiome in relation to fatty acid profiles revealed significant differences in the overall composition of the human milk microbiota between high (> 0.7% of total fat) and low (< 0.7%) trans-fatty acid groups (TF) (p = 0.039, pairwise PERMANOVA p = 0.035), high (> 40%) versus low (< 40%) saturated fatty acids (UniFrac p = 0.083, PERMANOVA p = 0.094), and high (>60%) versus low (<60%) unsaturated fatty acids (UF) (UniFrac p = 0.094, PERMANOVA p = 0.093). 84% of samples from omnivore mothers were in the high TF group compared to only 12% of samples from vegans. Gut-associated species (Faecalibacterium, Blautia, Roseburia and Subdoligranulum) and Lactobacillus were characteristic of both high UF and TF groups, but not the low-fat groups. Functional analysis revealed 2,4-dichlorophenol 6-monooxygenase was differentially abundant in the high UF group. Although microbiome diversity did not differ by diet type, TF breast milk content differed by diet group, highlighting the relationship between maternal diet and the microbial profile of human milk.

The objective of this study was to evaluate the effect of feeding Bacillus altitudinis spores to sows and/or offspring on growth and health indicators. On day (D) 100 of gestation, twenty-four sows were selected and grouped as: control (CON), fed with a standard diet; and probiotic (PRO), fed the standard diet supplemented with B. altitudinis WIT588 spores from D100 of gestation until weaning. Offspring (n 144) from each of the two sow treatments were assigned to either a CON (no probiotic) or PRO (B. altitudinis-supplemented) treatment for 28 d post-weaning (pw), resulting in four treatment groups: (1) CON/CON, non-probiotic-supplemented sow/non-probiotic-supplemented piglet; (2) CON/PRO, non-probiotic-supplemented sow/probiotic-supplemented piglet; (3) PRO/CON, probiotic-supplemented sow/non-probiotic-supplemented piglet and (4) PRO/PRO, probiotic-supplemented sow/probiotic-supplemented piglet. B. altitudinis WIT588 was detected in the faeces of probiotic-supplemented sows and their piglets, and in the faeces and intestine of probiotic-supplemented piglets. Colostrum from PRO sows had higher total solids (P = 0·02), protein (P = 0·04) and true protein (P = 0·05), and lower lactose (P < 0·01) than colostrum from CON sows. Maternal treatment improved offspring feed conversion ratio at D0-14 pw (P < 0·001) and increased offspring body weight at D105 and D127 pw (P = 0·01), carcass weight (P = 0·05) and kill-out percentage (P < 0·01). It also increased small intestinal absorptive capacity and impacted the haematological profile of sows and progeny. There was little impact of pw treatment on any of the parameters measured. Overall, the lifetime growth benefits in the offspring of B. altitudinis-supplemented sows offer considerable economic advantages for pig producers in search of alternatives to in-feed antibiotics/zinc oxide.

Health-related risk perceptions are important determinants of health behaviours and components of behaviour change theories. What someone thinks or feels will motivate or hinder their intention or hesitancy to implement a certain behaviour. Thus, a perceived potential risk to our health and well-being can influence our health-promoting and/or health-seeking behaviour. We aimed to review and synthesize available peer-reviewed literature to better understand the links between water and health-related risk perceptions and behaviours. We conducted the first systematic review of peer-reviewed literature on risk perceptions and behaviours in the context of water and health, published between 2000 and 2021. A total of 187 publications met the inclusion criteria. We extracted data relating to study characteristics and categorized our results according to the major themes emerging from the literature, namely drinking water, sanitation, hygiene and wasterelated topics, health risk factors, diseases and mental health implications, and preventative measures. Our review shows that the literature has grown over the past twenty years, reporting information from different countries belonging to different income groups around the globe, conducted in various settings and contexts, among different target populations, from various disciplinary angles, using different methods, theories and approaches. Our review provides evidence of health risk perceptions determining behaviour particularly related to drinking water sources and water safety. Evidence on disease prevention, health seeking, variations and changes in perception and behaviour over space, geography, socioeconomic differences and time, and the relevance of cultural context is provided. Our review shows that risk perception studies are vital for WASH governance in terms of policy, raising awareness, education and behaviour change. In order to make risk perception and behaviour studies even more relevant to effective public health planning and health messaging, future research needs to increasingly focus on early culturally sensitive interventions and changes in perceptions and behaviours over time.

Background. Our recent publication (Chey et al., Nutrients 2020) showed that a 30-day administration of pure galacto-oligosaccharides (GOS) significantly reduced symptoms and altered the fecal microbiome in patients with lactose intolerance (LI). Results. In this addendum, we performed an in-depth analysis of the fecal microbiome of the 377 LI patients randomized to one of two GOS doses (Low, 10–15 grams/day or High, 15–20 grams/day), or placebo in a multi-center, double-blinded, placebo-controlled trial. Sequencing of 16S rRNA amplicons was done on GOS or placebo groups at weeks zero (baseline), four (end of treatment), nine, 16 and 22. Taxa impacted by treatment and subsequent dairy consumption included lactose-fermenting species of Bifidobacterium, Lactobacillus, Lactococcus, and Streptococcus. Increased secondary fermentation microorganisms included Coprococcus and Ruminococcus species, Blautia producta, and Methanobrevibacterium. Finally, tertiary fermenters that use acetate to generate butyrate were also increased, including Faecalibacterium prausnitzii, Roseburia faecis, and C. eutactus. Conclusions. Results confirmed and expanded data on GOS microbiome modulation in LI individuals. Microbiome analysis at 16 and 22 weeks after treatment further suggested relatively long-term benefits when individuals continued consumption of dairy products.

The objective was to evaluate the effect of dietary Bacillus altitudinis spore supplementation during day (D)0–28 post-weaning (PW) and/or D29–56 PW compared with antibiotic and zinc oxide (AB + ZnO) supplementation on pig growth and gut microbiota. Eighty piglets were selected at weaning and randomly assigned to one of five dietary treatments: (1) negative control (Con/Con); (2) probiotic spores from D29–56 PW (Con/Pro); (3) probiotic spores from D0–28 PW (Pro/Con); (4) probiotic spores from D0–56 PW (Pro/Pro) and (5) AB + ZnO from D0–28 PW. Overall, compared with the AB + ZnO group, the Pro/Con group had lower body weight, average daily gain and feed intake and the Pro/Pro group tended to have lower daily gain and feed intake. However, none of these parameters differed between any of the probiotic-treated groups and the Con/Con group. Overall, AB + ZnO-supplemented pigs had higher Bacteroidaceae and Prevotellaceae and lower Lactobacillaceae and Spirochaetaceae abundance compared to the Con/Con group, which may help to explain improvements in growth between D15–28 PW. The butyrate-producing genera Agathobacter , Faecalibacterium and Roseburia were more abundant in the Pro/Con group compared with the Con/Con group on D35 PW. Thus, whilst supplementation with B. altitudinis did not enhance pig growth performance, it did have a subtle, albeit potentially beneficial, impact on the intestinal microbiota.

Eubacterium callanderi AMC0717 was isolated from the mucosa of the transverse colon of an 11-year-old organ donor. This strain contains genes putatively encoding short-chain fatty acids (SCFAs), exopolysaccharide (EPS), and several B vitamins.

ABSTRACTKnowledge of the intra-individual spatial and regional distribution of intestinal microbial populations is essential to understand gut host–microbial interactions. In this study, we performed a compositional analysis of luminal and mucosal samples from the small and large intestine of four organ donors by 16S rRNA amplicon sequencing and high-throughput quantitative polymerase chain reaction. Since the human microbiota is subject to selection pressure at lower taxonomic levels, we isolated over 400 bacterial strains and investigated strain-level variation of 11Lactobacillus rhamnosusfrom different intestinal regions. Results substantiate reported inter-individual variability as well as intra-individual differences along the gastrointestinal tract. Although the luminal and mucosal-associated communities were similar within individuals, relative abundance reflected the donors’ demographic and potential pathologies. The total bacterial load of all donors increased from small intestine to colon, whileBifidobacteriumwas in greater abundance in the small intestine. Comparative genomic analysis ofL. rhamnosusshowed the strains segregated into two distinct clusters and identified no features specific to location. Analysis revealed genetic differences for exopolysaccharide production, carbohydrate utilization, pilus formation and vitamin K biosynthesis between clusters. This study contributes to the understanding of niche-specific microbial communities, encouraging subsequent studies to better understand microbial signatures at lower taxonomic levels.

Citrobacter freundii AMC0703 was isolated from the intestinal mucosa of an 11-year-old organ donor. Genome analysis revealed the presence of multiple factors potentially aiding in pathogenicity, including fimbriae, flagella, and genes encoding resistance to fluoroquinolones, cephamycin, fosfomycin, and aminocoumarin.

ABSTRACT Knowledge of the intra-individual spatial and regional distribution of intestinal microbial populations is essential to understand gut host–microbial interactions. In this study, we performed a compositional analysis of luminal and mucosal samples from the small and large intestine of four organ donors by 16S rRNA amplicon sequencing and high-throughput quantitative polymerase chain reaction. Since the human microbiota is subject to selection pressure at lower taxonomic levels, we isolated over 400 bacterial strains and investigated strain-level variation of 11 Lactobacillus rhamnosus from different intestinal regions. Results substantiate reported inter-individual variability as well as intra-individual differences along the gastrointestinal tract. Although the luminal and mucosal-associated communities were similar within individuals, relative abundance reflected the donors’ demographic and potential pathologies. The total bacterial load of all donors increased from small intestine to colon, while Bifidobacterium was in greater abundance in the small intestine. Comparative genomic analysis of L. rhamnosus showed the strains segregated into two distinct clusters and identified no features specific to location. Analysis revealed genetic differences for exopolysaccharide production, carbohydrate utilization, pilus formation and vitamin K biosynthesis between clusters. This study contributes to the understanding of niche-specific microbial communities, encouraging subsequent studies to better understand microbial signatures at lower taxonomic levels.

Kombucha is a sweetened tea beverage that, as a consequence of fermentation, contains ethanol, carbon dioxide, a high concentration of acid (gluconic, acetic and lactic) as well as a number of other metabolites and is thought to contain a number of health-promoting components. The sucrose–tea solution is fermented by a symbiosis of bacteria and yeast embedded within a cellulosic pellicle, which forms a floating mat in the tea, and generates a new layer with each successful fermentation. The specific identity of the microbial populations present has been the focus of attention but, to date, the majority of studies have relied on culture-based analyses. To gain a more comprehensive insight into the kombucha microbiota we have carried out the first culture-independent, high-throughput sequencing analysis of the bacterial and fungal populations of 5 distinct pellicles as well as the resultant fermented kombucha at two time points. Following the analysis it was established that the major bacterial genus present was Gluconacetobacter, present at >85% in most samples, with only trace populations of Acetobacter detected (<2%). A prominent Lactobacillus population was also identified (up to 30%), with a number of sub-dominant genera, not previously associated with kombucha, also being revealed. The yeast populations were found to be dominated by Zygosaccharomyces at >95% in the fermented beverage, with a greater fungal diversity present in the cellulosic pellicle, including numerous species not identified in kombucha previously. Ultimately, this study represents the most accurate description of the microbiology of kombucha to date.

Fermentation is an ancient form of food preservation, which also improves the nutritional content of foods. In many regions of the world, fermented beverages have become known for their health-promoting attributes. In addition to harnessing traditional beverages for commercial use, there have recently been innovative efforts to develop non-dairy probiotic fermented beverages from a variety of substrates, including soy milk, whey, cereals and vegetable and fruit juices. On the basis of recent developments, it is anticipated that fermented beverages will continue to be a significant component within the functional food market.

Kefir is a fermented milk-based beverage to which a number of health-promoting properties have been attributed. The microbes responsible for the fermentation of milk to produce kefir consist of a complex association of bacteria and yeasts, bound within a polysaccharide matrix, known as the kefir grain. The consistency of this microbial population, and that present in the resultant beverage, has been the subject of a number of previous, almost exclusively culture-based, studies which have indicated differences depending on geographical location and culture conditions. However, culture-based identification studies are limited by virtue of only detecting species with the ability to grow on the specific medium used and thus culture-independent, molecular-based techniques offer the potential for a more comprehensive analysis of such communities. Here we describe a detailed investigation of the microbial population, both bacterial and fungal, of kefir, using high-throughput sequencing to analyse 25 kefir milks and associated grains sourced from 8 geographically distinct regions. This is the first occasion that this technology has been employed to investigate the fungal component of these populations or to reveal the microbial composition of such an extensive number of kefir grains or milks. As a result several genera and species not previously identified in kefir were revealed. Our analysis shows that the bacterial populations in kefir are dominated by 2 phyla, the Firmicutes and the Proteobacteria. It was also established that the fungal populations of kefir were dominated by the genera Kazachstania, Kluyveromyces and Naumovozyma, but that a variable sub-dominant population also exists.

Characterisation of the microbiota of traditional fermented beverages and screening these and other populations for novel antimicrobial producers and gene clusters Author(s) Marsh, Alan J. Publication date 2013 Original citation Marsh, A. J. 2013. Characterisation of the microbiota of traditional fermented beverages and screening these and other populations for novel antimicrobial producers and gene clusters. PhD Thesis, University College Cork. Type of publication Doctoral thesis Rights © 2013, Alan J. Marsh http://creativecommons.org/licenses/by-nc-nd/3.0/

Water kefir is a water-sucrose-based beverage, fermented by a symbiosis of bacteria and yeast to produce a final product that is lightly carbonated, acidic and that has a low alcohol percentage. The microorganisms present in water kefir are introduced via water kefir grains, which consist of a polysaccharide matrix in which the microorganisms are embedded. We aimed to provide a comprehensive sequencing-based analysis of the bacterial population of water kefir beverages and grains, while providing an initial insight into the corresponding fungal population. To facilitate this objective, four water kefirs were sourced from the UK, Canada and the United States. Culture-independent, high-throughput, sequencing-based analyses revealed that the bacterial fraction of each water kefir and grain was dominated by Zymomonas, an ethanol-producing bacterium, which has not previously been detected at such a scale. The other genera detected were representatives of the lactic acid bacteria and acetic acid bacteria. Our analysis of the fungal component established that it was comprised of the genera Dekkera, Hanseniaspora, Saccharomyces, Zygosaccharomyces, Torulaspora and Lachancea. This information will assist in the ultimate identification of the microorganisms responsible for the potentially health-promoting attributes of these beverages.

Imagine a world without antibiotics. A world where diseases such as syphilis, tuberculosis, meningitis were still commonplace, where a scrape on a leg could develop into life-threatening illness and the plague was still to be feared. Such was life before 1928, the year Alexander Fleming revolutionised the field of medicine by accidentally discovering penicillin, a mould which could kill bacteria. This drug became the world’s first antibiotic and it spurred scientists to discover other classes of antimicrobial compounds, which together dramatically reduced the spread of disease. However, this golden era of medicine will not last forever. After only a few years of use, disease-causing bacteria had emerged which were resistant to antibiotics. The most common of these so-called “superbugs”, methicillin-resistant Staphylococcus aureus (MRSA), is now responsible for an increasing number of deaths, and is practically untreatable. Similarly, incidents of multi- drug-resistant tuberculosis are on the rise. Other drug-resistant bacteria are ...

This chapter describes various strategies that can be used in identifying novel post-translationally modified, ribosomally synthesized, antimicrobial peptides. Their application in the discovery and evaluation of the lantibiotic family of antimicrobials is discussed.