The human intestinal microbiota is essential to the health of the host and plays a role in nutrition, development, metabolism, pathogen resistance, and regulation of immune responses. Antibiotics may disrupt these coevolved interactions, leading to acute or chronic disease in some individuals. Our understanding of antibiotic-associated disturbance of the microbiota has been limited by the poor sensitivity, inadequate resolution, and significant cost of current research methods. The use of pyrosequencing technology to generate large numbers of 16S rDNA sequence tags circumvents these limitations and has been shown to reveal previously unexplored aspects of the “rare biosphere.” We investigated the distal gut bacterial communities of three healthy humans before and after treatment with ciprofloxacin, obtaining more than 7,000 full-length rRNA sequences and over 900,000 pyrosequencing reads from two hypervariable regions of the rRNA gene. A companion paper in PLoS Genetics (see Huse et al., doi: 10.1371/journal.pgen.1000255) shows that the taxonomic information obtained with these methods is concordant. Pyrosequencing of the V6 and V3 variable regions identified 3,300–5,700 taxa that collectively accounted for over 99% of the variable region sequence tags that could be obtained from these samples. Ciprofloxacin treatment influenced the abundance of about a third of the bacterial taxa in the gut, decreasing the taxonomic richness, diversity, and evenness of the community. However, the magnitude of this effect varied among individuals, and some taxa showed interindividual variation in the response to ciprofloxacin. While differences of community composition between individuals were the largest source of variability between samples, we found that two unrelated individuals shared a surprising degree of community similarity. In all three individuals, the taxonomic composition of the community closely resembled its pretreatment state by 4 weeks after the end of treatment, but several taxa failed to recover within 6 months. These pervasive effects of ciprofloxacin on community composition contrast with the reports by participants of normal intestinal function and with prior assumptions of only modest effects of ciprofloxacin on the intestinal microbiota. These observations support the hypothesis of functional redundancy in the human gut microbiota. The rapid return to the pretreatment community composition is indicative of factors promoting community resilience, the nature of which deserves future investigation.

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The Pervasive Effects of an Antibiotic on the Human Gut Microbiota, as Revealed by Deep 16S rRNA Sequencing

The human gastrointestinal (GI) tract harbours a complex and dynamic population of microorganisms, the gut microbiota, which exert a marked influence on the host during homeostasis and disease Multiple factors contribute to the establishment of the human gut microbiota during infancy Diet is considered as one of the main drivers in shaping the gut microbiota across the life time Intestinal bacteria play a crucial role in maintaining immune and metabolic homeostasis and protecting against pathogens Altered gut bacterial composition (dysbiosis) has been associated with the pathogenesis of many inflammatory diseases and infections The interpretation of these studies relies on a better understanding of inter-individual variations, heterogeneity of bacterial communities along and across the GI tract, functional redundancy and the need to distinguish cause from effect in states of dysbiosis This review summarises our current understanding of the development and composition of the human GI microbiota, and its impact on gut integrity and host health, underlying the need for mechanistic studies focusing on host–microbe interactions

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Introduction to the human gut microbiota

Bacteria that colonize the mammalian intestine collectively possess a far larger repertoire of degradative enzymes and metabolic capabilities than their hosts. Microbial fermentation of complex non...

https://www.tandfonline.com/doi/pdf/10.4161/gmic.19897

Microbial degradation of complex carbohydrates in the gut

Alterations in the human intestinal microbiota are linked to conditions including inflammatory bowel disease, irritable bowel syndrome, and obesity. The microbiota also undergoes substantial changes at the extremes of life, in infants and older people, the ramifications of which are still being explored. We applied pyrosequencing of over 40,000 16S rRNA gene V4 region amplicons per subject to characterize the fecal microbiota in 161 subjects aged 65 y and older and 9 younger control subjects. The microbiota of each individual subject constituted a unique profile that was separable from all others. In 68% of the individuals, the microbiota was dominated by phylum Bacteroides, with an average proportion of 57% across all 161 baseline samples. Phylum Firmicutes had an average proportion of 40%. The proportions of some phyla and genera associated with disease or health also varied dramatically, including Proteobacteria, Actinobacteria, and Faecalibacteria. The core microbiota of elderly subjects was distinct from that previously established for younger adults, with a greater proportion of Bacteroides spp. and distinct abundance patterns of Clostridium groups. Analyses of 26 fecal microbiota datasets from 3-month follow-up samples indicated that in 85% of the subjects, the microbiota composition was more like the corresponding time-0 sample than any other dataset. We conclude that the fecal microbiota of the elderly shows temporal stability over limited time in the majority of subjects but is characterized by unusual phylum proportions and extreme variability.

https://www.pnas.org/content/pnas/108/Supplement_1/4586.full.pdf

Composition, variability, and temporal stability of the intestinal microbiota of the elderly

Background: Age-related physiological changes in the gastrointestinal tract, as well as modifications in lifestyle, nutritional behaviour, and functionality of the host immune system, inevitably affect the gut microbiota, resulting in a greater susceptibility to infections. Methodology/Principal Findings: By using the Human Intestinal Tract Chip (HITChip) and quantitative PCR of 16S rRNA genes of Bacteria and Archaea, we explored the age-related differences in the gut microbiota composition among young adults, elderly, and centenarians, i.e subjects who reached the extreme limits of the human lifespan, living for over 100 years. We observed that the microbial composition and diversity of the gut ecosystem of young adults and seventy-years old people is highly similar but differs significantly from that of the centenarians. After 100 years of symbiotic association with the human host, the microbiota is characterized by a rearrangement in the Firmicutes population and an enrichment in facultative anaerobes, notably pathobionts. The presence of such a compromised microbiota in the centenarians is associated with an increased inflammatory status, also known as inflammageing, as determined by a range of peripheral blood inflammatory markers. This may be explained by a remodelling of the centenarians’ microbiota, with a marked decrease in Faecalibacterium prauznitzii and relatives, symbiotic species with reported anti-inflammatory properties. As signature bacteria of the long life we identified specifically Eubacterium limosum and relatives that were more than ten-fold increased in the centenarians. Conclusions/Significance: We provide evidence for the fact that the ageing process deeply affects the structure of the human gut microbiota, as well as its homeostasis with the host’s immune system. Because of its crucial role in the host physiology and health status, age-related differences in the gut microbiota composition may be related to the progression of diseases and frailty in the elderly population.

/pdf/through-ageing-and-beyond-gut-microbiota-and-inflammatory-4g2ifzrqsv.pdf

Through Ageing, and Beyond: Gut Microbiota and Inflammatory Status in Seniors and Centenarians

The colonic microbiota mediates many cellular and molecular events in the host that are important to health. These processes can be affected in the elderly, because in some individuals, the composition and metabolic activities of the microbiota change with age. Detailed characterizations of the major groups of fecal bacteria in healthy young adults, in healthy elderly people, and in hospitalized elderly patients receiving antibiotics were made in this study, together with measurements of their metabolic activities, by analysis of fecal organic acid and ammonia concentrations. The results showed that total anaerobe numbers remained relatively constant in old people; however, individual bacterial genera changed markedly with age. Reductions in numbers of bacteroides and bifidobacteria in both elderly groups were accompanied by reduced species diversity. Bifidobacterial populations in particular showed marked variations in the dominant species, with Bifidobacterium angulatum and Bifidobacterium adolescentis being frequently isolated from the elderly and Bifidobacterium longum, Bifidobacterium catenulatum, Bifidobacterium boum, and Bifidobacterium infantis being detected only from the healthy young volunteers. Reductions in amylolytic activities of bacterial isolates in healthy elderly subjects and reduced short-chain fatty acid concentrations supported these findings, since bifidobacteria and bacteroides are important saccharolytic groups in the colon. Conversely, higher numbers of proteolytic bacteria were observed with feces samples from the antibiotic-treated elderly group, which were also associated with increased proteolytic species diversity (fusobacteria, clostridia, and propionibacteria). Other differences in the intestinal ecosystem in elderly subjects were observed, with alterations in the dominant clostridial species in combination with greater numbers of facultative anaerobes.

https://aem.asm.org/content/aem/70/10/6113.full.pdf

Comparison of compositions and metabolic activities of fecal microbiotas in young adults and in antibiotic-treated and non-antibiotic-treated elderly subjects

The human large intestine is covered with a protective mucus coating, which is heavily colonized by complex bacterial populations that are distinct from those in the gut lumen. Little is known of the composition and metabolic activities of these biofilms, although they are likely to play an important role in mucus breakdown. The aims of this study were to determine how intestinal bacteria colonize mucus and to study physiologic and enzymatic factors involved in the destruction of this glycoprotein. Colonization of mucin gels by fecal bacteria was studied in vitro, using a two-stage continuous culture system, simulating conditions of nutrient availability and limitation characteristic of the proximal (vessel 1) and distal (vessel 2) colon. The establishment of bacterial communities in mucin gels was investigated by selective culture methods, scanning electron microscopy, and confocal laser scanning microscopy, in association with fluorescently labeled 16S rRNA oligonucleotide probes. Gel samples were also taken for analysis of mucin-degrading enzymes and measurements of residual mucin sugars. Mucin gels were rapidly colonized by heterogeneous bacterial populations, especially members of the Bacteroides fragilis group, enterobacteria, and clostridia. Intestinal bacterial populations growing on mucin surfaces were shown to be phylogenetically and metabolically distinct from their planktonic counterparts.

Colonization of Mucin by Human Intestinal Bacteria and Establishment of Biofilm Communities in a Two-Stage Continuous Culture System

Background Because of changes in gut physiology, immune system reactivity, and diet, elderly people are more susceptible to gastrointestinal infections than are younger adults. The gut microflora, which provides a natural defense against invading microorganisms, changes in elderly people with the development of potentially damaging bacterial populations, which may lead to alterations in bacterial metabolism and higher levels of infection. Methods A randomized, double-blind, controlled feeding trial was done with 18 healthy elderly volunteers (age, >62 years) using a synbiotic comprising Bifidobacterium bifidum BB-02 and Bifidobacterium lactis BL-01 (probiotics) together with an inulin-based prebiotic (Synergy 1; Orafti). Real-time PCR was employed to quantitate total bifidobacteria, B. bifidum, and B. lactis in fecal DNA before, during, and after synbiotic consumption. Counting all viable anaerobes, bifidobacteria, and lactobacilli and identification of bacterial isolates to species level was also done. Results Throughout feeding, both bifidobacteria species were detected in fecal samples obtained from all subjects receiving the synbiotic, with significant increases in the number of copies of the 16S rRNA genes of B. bifidum, B. lactis, and total bifidobacteria, compared with the control week and the placebo group. At least 1 of these species remained detectable in fecal samples 3 weeks after feeding in individuals that had no fecal B. bifidum and/or B. lactis in the control week, indicating that the probiotics persisted in the volunteers. Counting of viable organisms showed significantly higher total numbers of fecal bifidobacteria, total numbers of lactobacilli, and numbers of B. bifidum during synbiotic feeding. Conclusion Synbiotic consumption increased the size and diversity of protective fecal bifidobacterial populations, which are often very much reduced in older people.

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Microbiological Effects of Consuming a Synbiotic Containing Bifidobacterium bifidum, Bifidobacterium lactis, and Oligofructose in Elderly Persons, Determined by Real-Time Polymerase Chain Reaction and Counting of Viable Bacteria

OBJECTIVE
The burden of chronic wounds did not disappear during the Covid-19 pandemic, so new ways to address healthcare practitioner (HCP) education had to evolve. The Teach, Try, and Talk (T3) programme was conceived in 2021 with HCPs in southern Europe (Italy, Spain and Portugal).


METHOD
Virtual education sessions with experienced HCP guest speakers were held and a five-layer hydrocellular polyurethane foam dressing (HPFD) was introduced as a way of reducing dressing change frequencies and improving clinician satisfaction. HCPs recorded their experience of the HPFD using an online form and participated in a further virtual session with experienced HCPs to discuss the results.


RESULTS
There were a total of 190 responses. A significant dressing change reduction from 3.6 changes per week to 1.8 with the HPFD (p<0.001) was observed in Italy, Spain and Portugal and within different care settings (hospital, wound clinic/health centre and the patient's home). Nearly one-third of participants stated one more day of dressing wear time was achieved by the ability of the HPFD to lock in and manage exudate, with nearly a quarter of responses stating it was due to fewer than three dressing lobes being full. The majority (97.8%) of HCPs stated they would recommend the HPFD to colleagues and patients.


CONCLUSION
The T3 programme is a highly successful method of training delivery and practice improvement across a variety of healthcare settings in southern Europe, helping support HCP engagement and ongoing development in challenging times during the Covid-19 pandemic. The programme can be adapted considering the needs of different HCPs and payor and/or healthcare systems.

Evaluation of a five-layer hydrocellular polyurethane foam dressing across wound care settings in southern Europe.

AIMS AND OBJECTIVES
Surveillance of wound infection including signs of infection alongside antimicrobial usage (types, duration, frequency) can highlight knowledge gaps and inconsistencies. This manuscript aims to highlight these, identify and inform opportunities for practice improvement and to show impact of infection management practice may be having on the issue of antimicrobial resistance.


BACKGROUND
Infected wounds pose challenges to healthcare professionals. Balancing risk of wound deterioration and progression to systemic infection with appropriate use of antimicrobials is necessary to minimise development of resistance.


METHODS
Analysis consisted of a practice survey of 9661 wounds across 70 community sites over a period of one week. Data were collected from projects between 2017 and 2020. The form was available to providers within the UK, Ireland, Norway, Denmark, Sweden and Finland. EQUATOR research guidelines were followed; STROBE checklist for observational research reporting was completed.


RESULTS
Infection rates of 8.9% were reported from wounds assessed. These data indicate inconsistencies with diagnosis across practice with non-specialists more likely to be unsure of wound infection. Greater confidence in infection identification was observed as number of signs increased. Inconsistencies were also observed in appropriate treatment; antimicrobials were used in 35% of wounds considered not infected and not used in 41% of wounds that were identified as infected.


CONCLUSIONS
This investigation of infection management practice of over 9000 wounds provides an insight into diagnosis and treatment of infection. Inconsistencies in diagnosis and treatment of wound infections reported highlight the need for increased education, awareness of diagnosis and treatment of infection.


RELEVANCE TO CLINICAL PRACTICE
Variability in management of infected wounds highlights opportunities to aid more effective diagnosis and treatment of infected wounds. Incorporation of support tools or evidence-based pathways into practice may enhance confidence in management of local infection, balanced with appropriate use, potentially minimising resistance and improving outcomes.

Emma J. Woodmansey

Papers

Comparison of compositions and metabolic activities of fecal microbiotas in young adults and in antibiotic-treated and non-antibiotic-treated elderly subjects

Colonization of Mucin by Human Intestinal Bacteria and Establishment of Biofilm Communities in a Two-Stage Continuous Culture System

Microbiological Effects of Consuming a Synbiotic Containing Bifidobacterium bifidum, Bifidobacterium lactis, and Oligofructose in Elderly Persons, Determined by Real-Time Polymerase Chain Reaction and Counting of Viable Bacteria

Evaluation of a five-layer hydrocellular polyurethane foam dressing across wound care settings in southern Europe.

Diagnosis and treatment of infected wounds: A multi-centre audit of current clinical practice across the UK, Ireland and Scandinavia.