Harry James Flint

• BSc, PhD
• Group Leader at University of Aberdeen

The microbial community of the human large intestine mainly ferments dietary fiber to short chain fatty acids (SCFAs), which are efficiently absorbed by the host. The three major SCFAs (acetate, propionate, and butyrate) have different fates within the body and different effects on health. A recent analysis of 10 human volunteer studies established...

The human colon contains a dynamic microbial community whose composition has important implications for human health. In this work, we build a process-based model of the colonic microbial ecosystem and compare with general empirical observations and the results of in vivo experiments. Our model comprises a complex microbial ecosystem along with abs...

The human colon contains a dynamic microbial community whose composition has important implications for human health. In this work we build a process-based model of the colonic microbial ecosystem and compare with general empirical observations and the results of in-vivo experiments. Based our previous work (Kettle et al., 2015), the microbial mode...

The human large intestinal microbiota thrives on dietary carbohydrates that are converted to a range of fermentation products. Short-chain fatty acids (acetate, propionate and butyrate) are the dominant fermentation acids that accumulate to high concentrations in the colon and they have health-promoting effects on the host. Although many gut microb...

Metabolites produced by microbial fermentation in the human intestine, especially short-chain fatty acids (SCFAs), are known to play important roles in colonic and systemic health. Our aim here was to advance our understanding of how and why their concentrations and proportions vary between individuals. We have analysed faecal concentrations of mic...

Lactate accumulation in the human gut is linked to a range of deleterious health impacts. However, lactate is consumed and converted to the beneficial short-chain fatty acids butyrate and propionate by indigenous lactate-utilizing bacteria. To better understand the underlying genetic basis for lactate utilization, transcriptomic analyses were perfo...

Lactate accumulation in the human gut is linked to a range of deleterious health impacts. However, lactate is consumed and converted to the beneficial short chain fatty acids butyrate and propionate by indigenous lactate-utilizing bacteria. To better understand the underlying genetic basis for lactate utilization, transcriptomic analysis was perfor...

Type IV pili (T4P) are bacterial surface‐exposed appendages that have been extensively studied in Gram‐negative pathogenic bacteria. Despite recent sequencing efforts, little is known regarding these structures in non‐pathogenic anaerobic Gram‐positive species, particularly commensals of the mammalian gut. Early studies revealed that T4P in two rum...

Background: The human colon is colonised by a dense microbial community whose species composition and metabolism are linked to health and disease. The main energy sources for colonic bacteria are dietary polysaccharides and oligosaccharides. These play a major role in modulating gut microbial composition and metabolism, which in turn can impact on...

Lactate is formed by many species of colonic bacteria, and can accumulate to high levels in the colons of inflammatory bowel disease subjects. Conversely, in healthy colons lactate is metabolized by lactate-utilizing species to the short-chain fatty acids butyrate and propionate, which are beneficial for the host. Here, we investigated the impact o...

Microbes in the intestinal tract have a strong influence on human health. Their fermentation of dietary nondigestible carbohydrates leads to the formation of health-promoting short-chain fatty acids, including butyrate, which is the main fuel for the colonic wall and has anticarcinogenic and anti-inflammatory properties. A good understanding of the...

Background: The composition of diets consumed following weight loss (WL) can have a significant impact on satiety and metabolic health. Objective: This study was designed to test the effects of including a nondigestible carbohydrate to achieve weight maintenance (WM) following a period of WL. Methods: Nineteen volunteers [11 females and 8 male...

While all regions of our digestive tract are colonized by micro-organisms to some degree, the densities, composition and nature of the associated microbial communities change markedly as we travel down through the gut (Fig. 5.1). The mouth (oral cavity) is well colonised, particularly the surfaces of teeth and crevices between the tooth and gum. As...

Most micro-organisms exist in nature as complex mixtures which are referred to as microbial communities. Members of such communities potentially interact with each other in various ways, including as competitors, predators and symbionts. Communities range from extremely dense mixtures of organisms that are held together in biofilms by binding to ea...

So far, we have tended to emphasise the benefits of symbiotic association between the host and its gut microbiota. On the other hand, we know only too well that micro-organisms and viruses pose a continual threat to the survival of multicellular life forms, and these micro-organisms include many that either inhabit, or pass through, our gut. A wide...

The term ‘Micro-organism’ refers to any living thing that is too small to be seen with the naked eye. It covers an astonishing array of life forms that began with the earliest living occupants of our planet. Of the three recognized domains of life, two (Bacteria and Archaea) consist exclusively of micro-organisms. The third (Eukaryota) contains all...

‘Molecular Biology’ has dominated the study of biology and microbiology since publication of the structure of DNA in the 1950s [1]. Right from the start, Molecular Biology, which focusses on the flow of genetic information from DNA to RNA to protein, produced staggering conceptual and technical advances. These included unravelling the genetic code...

We have seen how developments in molecular biology, chemical analysis and bioinformatics provide unprecedented new tools for analysing microbial communities and their activities. We have also seen how these are revealing the impact that microbial colonisation of the gut has on many aspects of human health (Fig. 12.1) [1]. So, perhaps the most obvio...

During natural childbirth the gut of the newborn infant becomes colonized with microorganisms that come mainly from the mother, although they can also come from the environment. In non-natural (i.e. caesarean, as opposed to vaginal) births there is less opportunity for the normal, messy routes of inoculation via faecal material and body fluids and...

Nearly all animals possess a digestive tract (the exception being parasites that live within their host’s tissues or digestive tracts) and in nearly all cases this consists of an open tube with flow of contents from one end (mouth or stoma) to the other (anus). Since the animal is ingesting food from its environment, it is also ingesting all of the...

In most living organisms, sugars play the central role in supplying energy for cellular activities via common pathways that start from glucose. In heterotrophs, which include all animals and many micro-organisms, sugars come from carbohydrates that are taken up from the surroundings or consumed in the diet. Autotrophic green plants, algae and cyano...

Background: The challenges for inflammatory bowel disease (IBD) diagnostics are to discriminate it from gut conditions with similar symptoms such as irritable bowel syndrome (IBS), to distinguish IBD subtypes, to predict disease progression, and to establish the risk to develop colorectal cancer (CRC). Alterations in gut microbiota have been propo...

A clone encoding carboxymethylcellulase activity was isolated during functional screening of a human gut metagenomic library using Lactococcus lactis MG1363 as heterologous host. The insert carried a glycoside hydrolase family 9 (GH9) catalytic domain with sequence similarity to a gene from Coprococcus eutactus ART55/1. Genome surveys indicated a l...

Obligate anaerobic bacteria from the genus Pectinatus have been known to cause beer spoilage for over 40 years. Whole genome sequencing was performed on eleven beer spoilage strains (nine Pectinatus frisingensis, one Pectinatus cerevisiiphilus and one Pectinatus haikarae isolate), as well as two pickle spoilage species (Pectinatus brassicae MB591 a...

Given the at times confusing new information concerning the human microbiome released over the last few years, this book seeks to put the research field into perspective for non-specialists. Addressing a timely topic, it breaks down recent research developments in a way that everyone with a scientific background can understand. The book discusses w...

Commensal butyrate-producing bacteria in the Firmicutes phylum are abundant in the human intestine and are important for maintaining health. However, understanding of the metabolism and host interaction of these bacteria is limited by the lack of genetic modification techniques. Here we establish a protocol enabling the transfer of autonomously-rep...

Fig. S3. Metabolite concentrations for the six fermentor experiments shown in Fig. S2. Blue arrows indicate the sampling points used for RNAseq analysis.

Fig. S4. KEGG Carbon metabolism pathway map for Blautia hydrogenotrophica. Genes present in the differentially expressed gene (DEG) list are highlighted with those with up regulated expression in the co‐culture compared to the mono‐culture in red and those with down regulated expression in green. Genes with KEGG orthologs found by KAAS‐KEGG, but no...

Table S2. RNAseq read counts.

Fig. S2. Growth (OD650) of Ruminococcus bromii, Blautia hydrogenotrophica and co‐cultures in continuous culture. Results are shown for six fermentors. Vessels R1 and C1 were inoculated simultaneously with R. bromii only (R1) or with both bacteria (C1) and supplied with RUM‐S medium containing 0.5% soluble starch. R2 and C2 refer to a repeat of this...

Table S4. Primers for qPCR.

Fig. S5. KEGG pathway map for metabolism of pantothenate and CoA in Blautia hydrogenotrophica. Genes present in the differentially expressed gene (DEG) list are highlighted with those with up regulated expression in the co‐culture compared to the mono‐culture in red and those with down regulated expression in green. Genes with KEGG orthologs found...

Table S1. Calculated carbon balances for monocultures and co‐cultures.

Table S3. Differentially expressed genes (DEGs) list from Ruminococcus bromii and Blautia hydrogenotrophica.

Fig. S1. Effect of formate on growth and metabolism of Blautia hydrogenotrophica in RUM medium. a) shows growth (OD650) with or without the addition of 10 mM formate and/or 0.2% (11 mM) glucose to the basal medium; b) and c) Metabolites formed and utilized during growth on glucose with or without formate (for the experiment shown in a). Values repr...

Dietary and host glycans shape the composition of the human gut microbiota with keystone carbohydrate-degrading species playing a critical role in maintaining the structure and function of gut microbial communities. Here, we focused on two major human gut symbionts, the mucin-degrader Ruminococcus gnavus ATCC 29149, and R. bromii L2-63, a keystone...

Interspecies cross‐feeding is a fundamental factor in anaerobic microbial communities. In the human colon formate is produced by many bacterial species but is normally detected only at low concentrations. Ruminococcus bromii produces formate, ethanol and acetate in approximately equal molar proportions in pure culture on RUM‐RS medium with 0.2% Nov...

Dietary fibers (DF) can prevent obesity in rodents fed a high-fat diet (HFD). Their mode of action is not fully elucidated, but the gut microbiota have been implicated. This study aimed to identify the effects of seven dietary fibers (barley beta-glucan, apple pectin, inulin, inulin acetate ester, inulin propionate ester, inulin butyrate ester or a...

The diversity of the colonic microbial community has been linked with health in adults and diet composition is one possible determinant of diversity. We used carefully controlled conditions in vitro to determine how the complexity and multiplicity of growth substrates influence species diversity of the human colonic microbiota. In each experiment,...

Productivity of ruminant livestock depends on the rumen microbiota, which ferment indigestible plant polysaccharides into nutrients used for growth. Understanding the functions carried out by the rumen microbiota is important for reducing greenhouse gas production by ruminants and for developing biofuels from lignocellulose. We present 410 cultured...

Fig. S4. Phylogenetic tree comparing the 30 cohesin modules from R. bromii L2‐63, L2‐36, 5AMG, ATCC27255 and YE282 strains.

Table S3. List of primers used for the different constructs produced.

Fig. S3. Activities of recombinant enzymes expressed in E. coli.

Fig. S5. Carbohydrate transport/utilization gene clusters in R. bromii genomes. Organization of (A) maltose and fructose transport systems and (B) glycogen biosynthesis gene cluster for the human Ruminococcus bromii L2‐63, L2‐36, ATCC27255 and 5AMG strains.

Fig. S6. Potential vancomycin resistance gene cluster in R. bromii L2‐63. (A), (B) This VanG cluster is present in R. bromii L2‐63 and L2‐36, but not in the other three genomes. However, we found no evidence for resistance to vancomycin in the two human strains that possess the VanG cluster compared with the two that lack the cluster (C).

Fig. S1. Pan genome analysis of the five R. bromii genomes. (A) Phylogenetic analysis using BPGA software based on concatenated core gene alignments. (B) COG distribution of core, accessory and unique genes of R. bromii strains as deduced by the pan‐genome analysis.

Table S1. Ruminococcus bromii genome assembly statistics.

Fig. S2. Phylogenetic tree of CBM37 modules from R. albus and ‘X’ modules from R. bromii.

Table S2. Distribution of GH, dockerins, cohesins and CBM modules in human and rumen Ruminococcus bromii strains

Data File S1. List of core, accessory and unique genes from pan‐genome analysis of 5 R. bromii strains.

Data File S2. List of locus tag numbers for amylase scaffoldin and dockerin genes for R. bromii L2‐63 strain before and after re‐annotation of the genome (Worksheet1), list of sporulation genes detected in R. bromii L2‐63 strain (Worksheet 2), conservation of L2‐63 sporulation genes in 4 other R. bromii strains (Worksheet 3), comparison of spore si...

The diet provides carbohydrates that are non-digestible in the upper gut and are major carbon and energy sources for the microbial community in the lower intestine, supporting a complex metabolic network. Fermentation produces the short-chain fatty acids (SCFAs) acetate, propionate and butyrate, which have health-promoting effects for the human hos...

Ruminococcus bromii is a dominant member of the human colonic microbiota that plays a ‘keystone' role in degrading dietary resistant starch. Recent evidence from one strain has uncovered a unique cell surface ‘amylosome' complex that organizes starch-degrading enzymes. New genome analysis presented here reveals further features of this complex and...

Technical variation in metagenomic analysis must be minimized to confidently assess the contributions of microbiota to human health. Here we tested 21 representative DNA extraction protocols on the same fecal samples and quantified differences in observed microbial community composition. We compared them with differences due to library preparation...

Dietary plant cell wall carbohydrates are important in modulating the composition and metabolism of the complex gut microbiota, which can impact on health. Pectin is a major component of plant cell walls. Based on studies in model systems and available bacterial isolates and genomes, the capacity to utilize pectins for growth is widespread among co...

A novel lanC-like sequence was identified from the dominant human gut bacterium Blautia obeum strain A2-162. This sequence was extended to reveal a putative lantibiotic operon with biosynthetic and transport genes, two sets of regulatory genes, immunity genes, three identical copies of a nisin-like lanA gene with an unusual leader peptide, and a fo...

Microbial communities perform highly dynamic and complex ecosystem functions that impact plants, animals and humans. Here we present an R‐package, microPop , which is a dynamic model based on a functional representation of different microbiota. microPop simulates the dynamics and interactions of microbial populations by solving a system of ordinary...

What we eat influences the species composition of our gut microbiota. This is not only because diet composition determines the supply of substrates for microbial growth (in the form of dietary residue, mainly fibre, that reaches the large intestine) but also because of impacts on gut transit and the gut environment. In turn the metabolic activities...

Protein-protein interactions play a vital role in cellular processes as exemplified by assembly of the intricate multi-enzyme cellulosome complex. Cellulosomes are assembled by selective high-affinity binding of enzyme-borne dockerin modules to repeated cohesin modules of structural proteins termed scaffoldins. Recent sequencing of the fiber-degrad...

The human gut microbiota ferments dietary non-digestible carbohydrates into short-chain fatty acids (SCFA). These microbial products are utilized by the host and propionate and butyrate in particular exert a range of health-promoting functions. Here we provide an overview of the metabolic pathways utilized by gut microbes to produce these two SCFA...

Ruminococcus champanellensis is a keystone species in the human gut that produces an intricate cellulosome system of various architectures. A variety of cellulosomal enzymes have been identified, which exhibit a range of hydrolytic activities on lignocellulosic substrates. We describe herein a unique R. champanellensis scaffoldin, ScaK, which is ex...

An altered intestinal microbiota composition is associated with insulin resistance and type 2 diabetes mellitus. We previously identified increased intestinal levels of Eubacterium hallii, an anaerobic bacterium belonging to the butyrate-producing Lachnospiraceae family, in metabolic syndrome subjects who received a faecal transplant from a lean do...

Table S1. Time sequence of bacterial colonization of wheat bran, from 454 sequence analysis of amplified 16S rRNA genes for four fermentor communities inoculated with human faecal microbiota. Table shows the proportional abundance and taxonomic classification for each OTU, and the LEfSe analysis (calculated using pooled solid and liquid sample data...

Table S2. Golay barcode sequences that were incorporated into the 16S rRNA gene primers that were used for each sample.

Fig. S1. Microbial colonization of wheat bran fibres following inoculation by mixed faecal microbiota. Images of wheat bran fibres following incubation with faecal inocula from two donors over time (h) using the FISH probes that detect all bacteria (Eub338) or Lachnospiraceae (Erec482).

Fig. S2. Impact of inter‐individual variation, and enrichment with wheat bran, on microbial community structure. Dendrogram, generated using the Bray–Curtis calculator in mothur, showing dissimilarities between microbial communities from each of the four donors at each time point, and the nine enriched Lachnospiraceae OTUs plus Bacteroides uniformi...

Fig. S3. Steps in ferulic acid conversion by the faecal microbiota. The major metabolites of ferulic acid detected in faecal samples (Russell et al., 2011) and in the fermentor experiments described in Fig. 4 are shown, together with reactions involved in their conversion. Abbreviations are given below the name of each compound.

During the last century, human nutrition has evolved from the definition of our nutritional needs and the identification of ways to meet them, to the identification of food components that can optimise our physiological and psychological functions. This development, which aims to ensure the welfare, health and reduced susceptibility to disease duri...

The importance of microbial communities (MCs) cannot be overstated. MCs underpin the biogeochemical cycles of the earth's soil, oceans and the atmosphere, and perform ecosystem functions that impact plants, animals and humans. Yet our ability to predict and manage the function of these highly complex, dynamically changing communities is limited. Bu...

The importance of microbial communities (MCs) cannot be overstated. MCs underpin the biogeochemical cycles of the earth’s soil, oceans, and the atmosphere, and perform ecosystem functions that impact plants, animals, and humans. Yet our ability to predict and manage the function of these highly complex dynamically changing communities is limited. B...

Supplementary Data

Dietary intake of specific non-digestible carbohydrates (including prebiotics) is increasingly seen as a highly effective approach for manipulating the composition and activities of the human gut microbiota to benefit health. Nevertheless, surprisingly little is known about the global response of the microbial community to particular carbohydrates....

During the last century, human nutrition has evolved from the definition of our nutritional needs and the identification of ways to meet them, to the identification of food components that can optimise our physiological and psychological functions. This development, which aims to ensure the welfare, health and reduced susceptibility to disease duri...

Firmicutes and Bacteroidetes are the predominant bacterial phyla colonizing the healthy human large intestine. Whilst both ferment dietary fibre, genes responsible for this important activity have been analysed only in the Bacteroidetes, with very little known about the Firmicutes. This work investigates the carbohydrate-active enzymes (CAZymes) in...

Cereal fibres such as wheat bran are considered to offer human health benefits via their impact on the intestinal microbiota. We show here by 16S rRNA gene-based community analysis that providing amylase-pretreated wheat bran as the sole added energy source to human intestinal microbial communities in anaerobic fermentors leads to the selective and...

We report here the complete genome sequence of the human gut symbiont Roseburia hominis A2-183 T (= DSM 16839 T = NCIMB 14029 T ), isolated from human feces. The genome is represented by a 3,592,125-bp chromosome with 3,405 coding sequences. A number of potential functions contributing to host-microbe interaction are identified.

Background: Faecalibacterium prausnitzii comprises 2 phylogroups, whose abundance in healthy and diseased gut and in conjunction with Escherichia coli has not yet been studied. This work aims to determine the contribution of F. prausnitzii phylogroups I and II in intestinal disease and to assess their potential diagnostic usefulness as biomarkers...

Faecalibacterium prausnitzii depletion in intestinal diseases has been extensively reported, but little is known about intra-species variability. This work aims to determine if subjects with gastrointestinal disease host different mucosa-associated F. prausnitzii populations from healthy individuals. A new species-specific polymerase chain reaction...

Cross-feeding is an important metabolic interaction mechanism of bacterial groups inhabiting the human colon and includes features such as the utilization of acetate by butyrate-producing bacteria as may occur between Bifidobacterium and Faecalibacterium genera. In this study we assessed the utilization of different carbon sources (glucose, starch,...

Unlabelled: Ruminococcus bromii is a dominant member of the human gut microbiota that plays a key role in releasing energy from dietary starches that escape digestion by host enzymes via its exceptional activity against particulate "resistant" starches. Genomic analysis of R. bromii shows that it is highly specialized, with 15 of its 21 glycoside...

We report here the complete genome sequence of a human gut symbiont Roseburia hominis A2-183T (=DSM 16839T=NCIMB 14029T), isolated from human faeces. The genome is represented by a 3,592,125 bp chromosome with 3,405 coding sequences. A number of potential functions contributing to host-microbe interaction are identified.

Ruminococcus champanellensis is considered a keystone species in the human gut that degrades microcrystalline cellulose efficiently and contains the genetic elements necessary for cellulosome production. The basic elements of its cellulosome architecture, mainly cohesin and dockerin modules from scaffoldins and enzyme-borne dockerins, have been cha...

Fae.ca.li.bac.te'ri.um. L. adj. faecalis pertaining to feces; Gr. dim. n. bakterion a small rod; N.L. neut. n. Faecalibacterium rod from feces, as this bacterium is abundant in feces, with the colon its presumed habitat. Firmicutes / “Clostridia” / Clostridiales / “Ruminococcaceae” / Faecalibacterium Variable length, straight, rod‐shaped cells (0.5...

Rose.bur'i.a. N.L. fem. n. Roseburia named in honor of Theodor Rosebury, an American microbiologist who studied and described micro‐organisms indigenous to humans. Firmicutes / “Clostridia” / Clostridiales / “Lachnospiraceae” / Roseburia Slightly curved, rod‐shaped cells (0.5 × 1.5–5 µm) occur singly and in (dividing) pairs. Nonsporulating. Gram‐ne...

Introduction: In England 67% of men and 57% of women are overweight or obese. Obesity is associated with multiple medical comorbidities. We set out to identify awareness of obesity among patients and secondary care clinicians, and promote healthier lifestyle through advice. Methods: We assayed all medical patients admitted to The Royal London Hospi...

Characterisation of the bacterial composition of the gut microbiota is increasingly carried out with a view to establish the role of different bacterial species in causation or prevention of disease. It is thus essential that the methods used to determine the microbial composition are robust. Here, several widely used molecular techniques were comp...