Although gut microbiota is by far the most investigated, the concepts of gut and blood microbiomes have grown in parallel since the early stages.

A Microbiome history: from gut microbiota to blood microbiome.

The presence of bacteria in blood has been shown as early as the 1680s’ while the dogma of blood sterility persisted for centuries. It has been increasingly challenged during the last century, leading to indisputable evidence.

 

Travel through the fascinating history of microbiota!

1680’s: First observations of fecal bacteria

Using his newly developed microscopes, Antonie van Leeuwenhoek described 5 different types of bacteria in feces and observed differences between health and disease.

1680’s: First observations of bacteria in the blood

Using his newly developed microscopes, Antonie van Leeuwenhoek observed erythrocytes and bacteria in salmon blood.

1850-1900: Founding work on host-microbe interactions

Pasteur, Metchnikoff, Koch, Escherich, Kendall and others laid the foundations of future human microbiota research. Koch developed the agar plate method to cultivate fecal bacteria and to analyze stools. Early on, Pasteur, Metchnikoff and Escherich foresaw the essential role of the endogenous flora for human health and the importance of understanding the interaction between non-pathogenic microorganisms and their host to comprehend the intestinal physiology and pathologies.

1917: Isolation of the first probiotic bacterial strain

Alfred Nissle isolated the first probiotic bacterial strain, Escherichia coli Nissle 1917, from a soldier who remained unafflicted during a dysentery outbreak and used it as a treatment. He later showed that this bacterial strain prevents the establishment of other pathogens through a colonization resistance mechanism.

1942: The blood sterility dogma is challenged

In his correspondence, M. R. Drennan questioned the meaning of sterility regarding blood. He stated that so far no argument met the required scientific standards to assert the absolute sterility of blood.

1944: The “Hungate technique” for culturing anaerobes

Robert E. Hungate revolutionized the culture of anaerobic bacteria with his roll-tube method and successfully cultivated Clostridium cellobioparus, a cellulose-degrading bacterium from bovine rumen. He published a complete description of his approach in 1950 and its adaptations to culture strictly anaerobic methanogens in 1969. (Hungate, J Bacteriol)

1958: Fecal microbiota transplantation to treat Clostridium difficile infection

After other treatments failed, four patients with pseudomembranous enterocolitis made a successful and rapid recovery after receiving fecal enema from healthy donors (Eiseman et al., Surgery). Fecal microbiota transplantation (FMT) is now widely recognized for helping with recurrent Clostridium difficile infections.

1965 : Transfer in germ-free mice of intestinal bacteria

Schadler and colleagues fed germ-free (GF) mice with cultures of several anaerobic bacteria isolated from conventional mice and showed the stability of such microbial transfers for several months as well as the reduction of the typical caecum enlargement in GF mice and their offspring (Schadler et al., J Exp Med)

1970: Growing L-form bacteria in arthritic subjects

Pease observed L-form bacteria growing in association with erythrocytes in arthritic patients. (Pease, Ann Rheum Dis)

1972: L-form bacteria in the blood of healthy subjects

Tedeschi and Amici identified L-form bacteria in the blood of healthy subjects (Tedeschi and Amici, Ann Sclavo)

1976: Staphylococcus epidermidis in the blood of healthy and thrombocytopenic subjects

Tedeschi and colleagues identified several strains of Staphylococcus epidermidis in the blood of both healthy and thrombocytopenic subjects (Tedeschi et al., Experientia)

1977: Novel bacterial structure isolated in human blood

From diseased and healthy human blood, novel bacterial structures were microscopically observed and cultured by Domingue and Schlegel (Infection and Immunity).

1978: More evidence of the association between bacteria and erythrocytes

Corynebacteria-like microorganisms were observed within human erythrocytes by electron microscopy (Tedeschi et al., Experientia).

1981: Microbial acquisition and maturation in early life

Early studies described some components of the microbial succession in early life, but in 1981 three landmark studies quantitatively characterized the gut microbiota acquisition in infants and how it is shaped by feeding (Rotimi and Duerden, J Med Microbiol / Tompkins et al., J Hyg / Daoulas et al., Arch Fr Pediatr).

1996: First 16S rRNA gene sequencing study of the fecal microbiome

Thanks to the pioneering work of Woese, Pace and others to identify environmental bacteria, Wilson and Blitchington used the 16S rRNA gene sequencing approach to compare cultivated and non-cultivated bacteria in human feces. The bacterial diversity inhabiting the human gut was so far largely underestimated due to the inability to cultivate a large fraction of the microorganisms. (Wilson and Blitchington, Appl Environ Microbiol)

1998: Inter-individual variations and temporal stability of the gut microbiota

Several studies showed strong relationships between microbiota dysbiosis and diseases leading to the question “what is a healthy microbiota and, what are the normal variations?” A study by the De Vos group first revealed, using a molecular fingerprint approach, the individuality of the microbiota and its stability over time in adults (Zoetendal et al., Appl Environ Microbiol). Much is still unknown regarding the description of a healthy core microbiota and its “normal” dynamics.

2001: First confirmation of the bacterial DNA presence in the blood of healthy humans

Nikkari and colleagues detected bacterial DNA in the blood of four healthy subjects thanks to quantitative PCR using primers and probe specific to the bacterial 16S rRNA gene (Nikkari  et al., J Clin Microbiol)

2002: Bacteria are naturally occurring in the blood of healthy subjects

Viable pleomorphic bacteria were detected by fluorescent in situ hybridization and flow cytometry, and further characterized using a molecular approach targeting their 16S rRNA and gyrB genes (McLaughlin et al., J Clin Microbiol)

2004: Gut microbiota regulates the mucosa immunity

Historically, the relationship between the immune system and bacteria was only seen as antagonistic and through the host defense against pathogens. Early studies in germ-free animal models suggested the education of the immune system by infections. Rakoff-Nahoum and colleagues showed that under physiological conditions, the immune system recognizes microbiota commensals through PRRs (Pattern Recognition Receptors) and that this mechanism is essential for tissue repair (Rakoff-Nahum et al., Cell). This study opened a new perspective on the beneficial and symbiotic role of microbiota-immune system interactions.

2005: Diet and gut microbiome

From blood samples of 60 healthy donors, 35% of the red blood cell fractions and 53% of the plasma-fractions gave positive bacterial cultures, bringing more evidence that at least some members of the healthy blood microbiota are alive and viable (Damgaard et al., PLoSOne).

2006: The host-phenotype is transmissible through fecal microbiota transplantation

Turnbaugh and colleagues showed that the obese microbiome harvests more energy from the diet and that the obese phenotype is transferable from obese to lean mice through fecal microbiota transplantation (Turnbaugh et al., Nature). This study confirmed the underlying contribution of the gut microbiome to the pathophysiology of obesity.

2007: The Human Microbiome Project (HMP)

The National Institutes of Health launched the HMP, a US community resource program aiming to provide widely available and reliable clinical, analytical and computational tools and protocols. The phase 1 (2008-2012) surveyed the microbiome of 5 major habitats among 242 donors to evaluate whether host health status can be associated with a specific microbial signature.

2008: The Metagenomics of the Human Intestinal Tract consortium (MetaHIT)

Funded by the European Union, the MetaHIT consortium gathered 13 partners from 8 countries (Denmark, France, Germany, Italy, Netherlands, Spain, United Kingdom and China) to establish an extensive catalog of genes and genomes of the human intestinal microbiota in health and diseases (inflammatory bowel diseases and obesity).

2008: Further molecular evidence of the circulating microbiome

The blood microbiome from two healthy individuals was described by 16S rRNA gene sequencing using the Sanger technology. Negative controls were performed and did not produce visible PCR products (Moriyama et al., Microbiol Immunol)

2010: Microbiome metagenomics in a large human population

Thanks to the advances in high-throughput sequencing, the MetaHIT consortium published an extensive gene catalog of the fecal microbiome in a large human cohort of 124 European adults. Qin and colleagues evaluated that the entire cohort harbored around 1,150 bacterial species with the microbiota of each individual comprising at least 160 species (Qin et al., Nature).

2011: The importance of the microbiota in the gut-brain axis

Several studies in mouse models showed the gut microbiota effects on behavior, gene expression in the brain and the development of the nervous system and suggested the influence of the gut microbiome on the critical period of brain development (Diaz Heijtz et al., PNAS / Neufeld et al., Neurogastroenterol Motil / Berick et al., Gastroenterol / Bravo et al., PNAS).

2011: The involvement of bacterial translocation in the early onset of Type 2 diabetes

For the first time, Amar and colleagues demonstrated in murine models the missing link between compositional changes in gut microbiota and the onset of type 2 diabetes. Mice fed with a high-fat diet showed an exaggerated bacterial translocation and so, an increased bacterial content in mesenteric adipose tissue inducing inflammation and leading to insulin resistance (Amar et al., EMBO). 

The same year, Amar and colleagues established in humans the involvement of tissue bacteria in the onset of diabetes. In a longitudinal study on the D.E.S.I.R. (Epidemiological Study on the Insulin Resistance Syndrome) cohort, they showed that the blood microbiome is an independent marker of the risk of diabetes (Amar et al., Diabetologia).

2013: The launch of the HMP phase 2 (iHMP) and microbiome-immune system interactions

The phase 2 of the HMP project (2013-2016) called the integrative HMP aimed to integrate longitudinal and multi-omics data from both the microbiome and the host in pregnancy, preterm birth and the onset of inflammatory bowel diseases and type 2 diabetes. 

Three compelling studies also showed that the short-chain fatty acids derived from the gut microbiota promote the production of regulatory T cells, crucial for the immune homeostasis (Smith et al., Science / Atarashi et al., Nature / Arpaia et al., Nature).

2015: Interaction between host-targeted drugs and gut microbiota

Several studies observed an impact of commonly used medication like metformin and proton-pump inhibitors on the gut microbial communities and bacterial gene expression, which may have beneficial or harmful effects on human health (Tsuda et al., Clin Transl Gastroenterol / Freedberg et al., Gastroenterology / Forslund et al., Nature). Indeed, the Zitvogel’s group showed that the efficiency of cancer immunotherapy depends on distinct Bacteroides species. No antitumor effects of CTLA-4 blockade were observed in antibiotic-treated or germ-free mice (Vétizou et al., Science).

2015: More evidence of bacterial growth from healthy human blood

From blood samples of 60 healthy donors, 35% of the red blood cell fractions and 53% of the plasma-fractions gave positive bacterial cultures, bringing more evidence that at least some members of the healthy blood microbiota are alive and viable (Damgaard et al., PLoSOne).

2016: The amount of bacterial DNA and the profile of the blood microbiota differs amongst blood fractions

Using 16S rRNA gene targeted quantitative PCR, Païssé and colleagues showed that more than 90% of the bacterial DNA is located in the buffy coat and around 6% in the red blood cells, while the plasma contains less than 0.1%. The microbiome associated with each fraction was described using 16S rRNA gene sequencing and showed the presence of a highly diversified blood microbiome in healthy donors (Païssé et al., Transfusion).

2018: Human gut microbiome modulates the response to cancer therapy

Following earlier preclinical studies in murine models, several human studies showed an association between gut microbiome and response to immunotherapy in cancer patients. Metagenomic studies revealed differences in bacterial diversity and functions in responding patients, suggesting an enhanced systemic and antitumor immunity with a favorable gut microbiome (Routy et al., Science / Gopalakrishnan et al., Science / Matson et al., Science)

2018: Multiplication of the characterizationS of the blood microbiome in health and disease

Several studies described the blood microbiota using molecular and/or cultural approaches in healthy subjects. Schierwagen and colleagues reported the characterization of the circulating microbiome in portal, hepatic, atrium and peripheral blood showing the specificity of each circulatory compartments. This study raised concerns regarding the risk of describing contaminants in low biomass samples. Schierwagen and colleagues rebutted these concerns by publishing the results from the negative controls carried through the entire workflow. These results undoubtedly confirmed the description of the circulating microbiome (Schierwagen et al., Gut).

2020: Towards the recognition of blood and tissue microbiomes and their involvement in human pathologies

With the multiplication of publications properly addressing the negative controls, blood and tissue microbiomes are finally recognized as new exciting research paths that could lead to considerable clinical advances. Anhê and colleagues showed how the bacterial tissue compartmentalization in adipose tissue and liver is modulated by type 2 diabetes in human obesity. This study was applauded as a true game-changer for the field of microbiome research and for understanding how microbiomes influence human health and diseases (Cani and Van Hul, Nature Metabolism).

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Benjamin LELOUVIER
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