每个人的一生都会经历很多，从出生到长大，健康到衰老疾病。你的出生、遗传、家庭环境、很大程度上决定的人生起点，日常的饮食、行为习惯决定你的身体成长，一些不同的选择或意外的事件又会让人生有很多起伏和不同。
每个人的菌群和我们的人生一样也是独一无二的，我们菌群的特点反映着不同人各自生活的烙印。从母亲的腹中开始影响和决定了我们最初的菌群，出生方式、喂养的食物、用药等都决定了我们的菌群基数。当我们开始从喝奶到开始摄入辅食，我们的菌群也同样迎来巨大的演变。当我们生病、感染、运动、饮食、社交、虚弱、衰老这些同样反映在我们菌群的变化和演替上。
相对的，当我们更多的了解我们的菌群，善待和改善它们，同样的变化也会出现在我们的身体和生活中。 A growing body of evidence suggests a strong association between age and the human microbiota, with the gut microbiota at the heart of many age-related changes, including immune system dysregulation and disease susceptibility. The microbial composition of several body parts can predict age in humans with relative accuracy.
In the Guhe Healthy Intestinal Microbiota Detection Database, there is also a prediction of intestinal age:
Diagram of the health-intestinal age prediction model of Guhe grain
<来源：谷禾健康肠道菌群数据库>
It can be seen that the intestinal age and physiological age are basically consistent. The age of the intestinal microbiota of healthy people is precisely the most consistent with the real age, and a large difference from the real age means that the intestinal flora is deviated.
Healthy people have a more diverse and balanced gut flora. Age-related changes in the microbiota are attributed to physiology, lifestyle, and health status. Each of these factors is associated with changes in the relative abundance of certain flora.
For example, diet, hygiene, siblings, pets, allergies, childhood illnesses, and antibiotics are some of the prominent factors that affect a child's microbiome. In adulthood, the microbiota is relatively stable, while in old age, some beneficial bacteria begin to decline gradually, and the microbiota transitions to another stage.
At every stage of life, from birth to death and decomposition, the microbial community is a dynamic component of the body. Studying natural and induced changes in the microbiota has the potential to revolutionize our understanding of human biology.
This article describes how the microbiota changes in a healthy person over a lifetime, discussing the stages of microbial expansion, from the composition of the microbiota at birth, to the changes in disease or antibiotic use, to the expansion of the microbiota at death, and the differences in body parts and composition (bacterial, fungal, or viral) of these stages. Understand future research directions on the relationship between the microbiota and age, so as to gain a better understanding of the human microbiota and interventions based on it.
01
The microbiota in the human body
The microbial community is present on the surface of every mucous membrane of the human body, and each body part of the human body has a unique ecology. Each person's microbiome, like a fingerprint, is unique.
Within individuals, specific body parts, geographic locations, and the age of individuals are strongly associated with a healthy microbiome. Age-driven α diversity and β diversity of the human microbiota.
Before we understand the changes in the microbiota at each stage, let's understand one concept: microbial succession.
Microbial succession refers to changes in the presence, relative abundance, or absolute abundance of one or more organisms in a microbial community.
During normal or healthy aging, the three main stages of microbial succession occur naturally in human life.
Three distinct stages of microbiota change
✦ Primary succession (colonization of the pioneer flora at birth, rapid changes until late childhood)
The first stage, primary succession, begins when the pioneer species first establishes a community, followed by rapid changes in the microbial community. From birth to childhood, the rate of change decreases, and many intermediate species exist between birth and late childhood.
Primary succession ends with the formation of an apex community, which is achieved during adolescence and continues to a large extent into adulthood;
While the microbiota in adulthood is more stable than in childhood, there is still variation, which has sparked debate about whether there is a top community in the human microbiota. Natural variation in the adult microbiota exists on a time scale from hours (circadian rhythm) to years (aging), but the microbiota is relatively stable unless there is a disturbance, such as a change in diet or medications.
✦ Secondary succession (change of flora, reconstruction)
The next stage, secondary succession, occurs after a part of a pre-existing stable community has been altered or removed, and then the community regenerates into the same state or a different state. This can be achieved human-based through medical treatments such as antibiotics, or spontaneously through diseases such as Vibrio cholerae infection.
Secondary succession in humans is characterized by random processes dominating for at least a period of time. Under induction conditions, such as a single course of antibiotics, the community follows a process similar to primary succession, in which a portion of the existing microbial community acts as "microbial memory", helping to reconstruct a community similar to a previously existing one.
This process is thought to be driven by the core microbiota rather than the pioneer microorganisms that drive the primary succession.
✦ End-stage succession (natural aging and death stages)
The eventual terminal succession is part of the host's natural aging and death. In old age, the microbial community again at a higher rate of change, successfully yielding a community of fewer members, often with an increase in the relative abundance of the phylum Proteobacteria (also known as Pseudomonas), sometimes as a total predominant.
Studying each stage of succession allows researchers to address how microbial communities associated with humans are formed and maintained. By understanding these processes, we can better understand how the microbiome changes with age and how it relates to human health, and how to manage the microbiota.
Changes in the relevant microbiota in humans from conception to death
Martino C,et al. Nat Rev Microbiol.2022
The diversity of resident bacteria, fungi, and viruses changes at all stages of human life. The analog clock represents the relative time of the host age of development at each microbial community stage.
Immunoimprinting begins before birth through the mother's microbiota and its metabolites (first column). Initial colonization of pioneer species begins at birth with the emergence of specific microbial communities in body parts (second column). The complexity of these communities increases until they reach a relatively stable community structure (third and fourth columns).
Secondary succession of these microbial communities may arise from internal and external disturbances (column 5). The intermediate microorganisms re-establish the initial colony and reach a steady state again (columns 6 and 7).
In later years, as the host approaches natural death, the community undergoes its final succession and change (column 8). The final stage of microbial succession occurs in the spoilage and decomposition phase. At this stage, diversity declines further, and for the first 24-48 hours, many human microbiota structures remain unchanged, but soon begin to erode and decompose (column 9).
The green and blue lines show the relative strength of adaptive immunity and innate immunity at different stages of microbial succession, respectively.
Bacterial diversity measurements at different age groups
Martino C,et al. Nat Rev Microbiol.2022
A U.S. gut project focused on measuring bacterial diversity and phylogenetic history of human fecal (part a), oral (part b), and skin (part c) microbiota from childhood to old age, containing 21,919 fecal, 1,920 oral, and 998 skin microbiota samples with 16S ribosomal RNA gene amplicon sequences.
α diversity, a quantitative measure of the number of different types of microorganisms in a sample, measured across ages through Faith's phylogenetic diversity (PD) α diversity measure.
UniFrac β Diversity Principal Coordinate Analysis, a method for comparing the similarity of microbial communities, where spatially close points represent similar samples and spatially distant points represent different samples, colored by age.
02
The "Pioneer Flora" in Early Life
✦Fetal period - microbiota and metabolites affect immune development
The first factor that shapes the human microbiome comes from the mother during fetal development.
Through the placenta, the fetus is exposed to metabolites produced by the mother's microbiome, which affect its immune system and affect aspects of the normal microbiota and later pathology. Metabolites, such as short-chain fatty acids (acetate) and other microbial compounds, can be transferred to the fetus through the placenta and affect immune development. The mother's diet and health can also affect these metabolites.
Acetate in fetal tissue affects epigenetic imprinting associated with regulatory T cell production in adults, which is associated with preventing the development of asthma later in life.
✦ After birth – the microbiota is affected by birth patterns, diet, environment, etc
After birth, the microbial community rapidly differentiates based on body parts.
In the initial phase, pioneer species and community development over the next 4 years may be influenced by birth patterns and gestation duration. Intermediate communities are influenced by diet, such as the consumption of breast milk or formula, as well as the environment.
Finally, the diet and environment once again shaped a stable apex community. It is mainly composed of fungi, bacteria, and viruses.
Major succession in utero and early life
Microbial metabolites and ligands regulate host aryl hydrocarbon receptors, which help shape neonatal microbial and immune development. Maternal antibiotic use and gastrointestinal-related diseases, such as inflammatory bowel disease, are also thought to increase the risk of pathology in offspring through imprinting of the fetal immune system.
However, these links have only been studied in non-human experiments. In one case, germ-free mice colonized by the microbiota of pregnant women with inflammatory bowel disease or their newborns continued to develop abnormal microbiota and immune development indicative of inflammatory bowel disease.
✦ Changes in the mother's microbiota and immune system during pregnancy
During pregnancy, the mother's microbiota and immune system are also altered. The mother's vaginal microbiota becomes more diverse, often consisting of many microbiota found in other body parts.
During pregnancy, the maternal immune system forms synergies with the fetus, including the transfer of IgG antibodies through the placenta.
Colonization of neonatal pioneer bacteria
There is some controversy as to whether the microbiota acquired at birth is derived from the vagina and feces through a mixture, or whether the vaginal microbiota itself is pluripotent at birth and is the primary source of microbial pioneers.
Regardless of the exact maternal origin, this stage is characterized by pioneer bacterial species. The following flora are included:
- Lactobacillus
- Enterobacter
- Escherichia
- Bacteroides
- Parabacteroides
- Prevotella
These bacteria then settle in regular body parts: the intestines, mouth, and skin.
Many pioneer bacteria are facultative anaerobes that consume oxygen, thus enabling obligate anaerobes to colonize each environment later on. At first, every body part of the newborn is relatively undifferentiated, but pioneer microbes soon begin to initiate a cascade of body-dependent microbial diversity, and bacteria at each site can be easily distinguished by bacteria at least by the 4th to 6th week of life.
After the arrival of pioneer bacteria, the microbiota of early life gradually begins to form. In the following sections, we will look at the microbiota (including bacteria, fungi, viruses, etc.) in the intestines, mouth, skin, and other parts of early life.
03
Characteristics of microbiota in early life
Gut microbiota
✦ Intestinal flora – Bifidobacteria dominate
The development of the human gut bacterial community has been well studied.
Bifidobacteria spp. were dominant until at the end of the first year of life, when they were replaced by a combination of Bifidobacteria, Clostridium, and Bacteroidetes. The abundance of Bacteroides increased while species such as Bifidobacteria decreased comparatively.
Bifidobacteria break down human milk oligosaccharides and develop them to affect the immune system
Recently, a study found that bacteria such as Bifidobacteria contain genes required for the catabolism of human milk oligosaccharides, and there is a functional link between immune development in infants. In particular, the feces of infants receiving Bifidobacterium infantis EVC001 polarized naïve T cells differed from those from the control group in a manner associated with reduced intestinal inflammation.
Other species can also degrade human milk oligosaccharides (e.g., Bacteroides, Ackermansia bacteria)
By the age of 3-6 years, the gut bacterial community converges into a sustained apex community throughout adulthood. This microbiota is one of the densest and most diverse ecological communities known. Usually, during this time, only two bacterial phyla predominate in the average healthy person: Firmicutes and Bacteroidetes.
✦ Other intestinal microbiota – fungi, archaea, viruses
During the development of the human gut, the virome, fungal and archaeal groups have been studied far less than the bacterial group. Throughout the life cycle, fungal communities account for much less total than bacterial or viral groups.
Fungal communities
The fungal community contains large amounts of Rhodotorula and Debaryomyces in the first few days of life, and the following month Candida, Cryptococcus and Saccharomyces spp.
到成年时,主要的真菌属是Aspergillus, Candida和Saccharomyces。
Archaeal bacterial communities
The archaeal community of the gut during development is unknown, but archaea are some of the earliest transmigrant colonies, but they are less abundant.
早期定植的古细菌包括Methanosphaera和Methanobrevibacter。
Viral Community: The bacteriophage family becomes endemic after birth
The viral community, which consists mainly of bacteriophages, is abundant in the first week of life. The phage families Siphoviridae, Podoviridae, and Myoviridae are prevalent immediately after birth and are mainly integrated into the bacterial genome in lysogenic form.
By the fourth month of life, there is a massive growth of the order Certiculus phages, and the members are more often lysed (infectious phage granules or actively replicating phages).
In adults, Caudovirales and Microviridae predominate in the intestinal phage community, but the phage enterovirome is highly specific to individuals, and its succession remains largely unknown.
Unlike bacteriophages, the enterovirome infected with eukaryotic viruses is primarily associated with pathology in children and adults. Recently, low abundance of some eukaryotic virus-infecting cells has also been observed in healthy children and healthy adults, but the timing and prevalence of their occurrence are unknown.
Oral microbiota
✦ Oral microflora: gradually stabilizes in the first few months of life, and transforms again after tooth formation
At birth, the oral flora has a high prevalence in the following genera:
- Streptococcus
- Twin
- Granulicatella
- Veillonella
In the following months, Lactobacillus and Fusobacterium also became popular. The abundance of Staphylococcus peaks around 3 months after birth and then steadily declines, giving way to the higher abundance of Gemella, Granulicatella, Haemophilus and Rothia spp.
牙齿形成后，口腔微生物群再次转变，在成年期具有更高丰度的梭杆菌门， Synergistetes, Tenericutes, Saccharibacteria (TM7), SR1 。
✦ Other microorganisms in the oral cavity: The adult oral cavity contains methanogens, and the most common phage group is caudate virus
The oral fungal community is thought to have less fungal diversity than the skin and internal organs. Candida spp. was one of the first fungal colonizing fungi in the oral cavity. Little is known about the intermediate oral fungal community, but adults Candida, Cladosporium, Aureobasidium,
Aspergillus,Fusarium和Cryptococcus spp.的丰度较高。
The oral archaea during development are unknown, but the adult oral cavity contains many archaeal methanogens, including Methanobacterium spp.
Little is currently known about viruses in the oral cavity of human infants. In adults, similar to the gut, the most common group of phages is caudate virus.
Oral viral populations are generally considered pathological in nature (e.g., coxsackie-A virus, measles virus, erythrovirus, and human papillomavirus), and no longitudinal studies have been conducted on viral community composition. However, many eukaryotic virus taxa have also been observed in asymptomatic and healthy adults.
Skin microbiota
✦ Skin bacterial community: Lactobacillus vaginalis is more common in the mother at birth, similar to that of an adult at 4-5 weeks
The skin bacterial community is born with a high amount of the maternal Lactobacillus vaginalis. By 4-5 weeks, the infant skin microbiota is similar to the adult skin microbiota but continues to become more site-specific during adolescence.
Staphylococcus and Corynebacterium at different sites Pseudomonas, Enterobacter, Enterococcus,
Proteus和Klebsiella在特定位点(如腋窝与前臂)。
✦ Other microorganisms in the skin: Malassezia has a relatively high proportion, and archaea account for about 4%.
Among the dermatofungal communities, Malassezia, Candida and Saccharomyces are most prevalent in the first 30 days of life. Little is known about the exact composition of the intermediate community, but the abundance of Malassezia is generally high in adult fungal communities, estimated to account for about 75% to 90% of the total composition of the fungal community.
Less is known about the development of the skin archaeal community, but archaea make up about 4% of the adult microbiota. In general, the adult skin archaea are represented by the phylum Thaumarchaeota and the phylum Euryarchaeota. Halobacteriaceae and Methanobrevibacter are also found on adult skin.
Unlike the gut and oral cavity, healthy skin microbiota possesses relatively little known viral diversity and is rarely studied, possibly due to technical limitations associated with low biomass samples. However, there are some naturally occurring groups of viruses on the skin.
Knowing about the microbiota of the gut, mouth and skin in early life, what factors will affect the development of microbiota in early life?
Factors influencing the development of early microbial communities
In the first years of life, there are several factors that shape and distinguish the development of microbial communities.
✦ Birth mode and maternal antibiotic use
Birth mode and maternal antibiotic use are among the best-studied and clearest factors influencing human microbiomes. However, the development of microorganisms can lead to unique results, even in cohabiting identical twins, which may be due to a number of unknown or random processes.
Through caesarean section and perinatal and neonatal antibiotic exposure, the process of establishing a natural microbial community may be disturbed in all body parts. This finding highlights the importance of the vaginal microbiome, which naturally contains a large amount of Lactobacillus spp., but is altered during puberty and is essential for women's health.
SOME OF THE BEST SAMPLE OF INFANT DEVELOPMENT STUDIES, OFTEN ABBREVIATED AS DIABIMMUNE ECAM AND TEDDY, WERE FOLLOWED UP FOR THE FIRST 2 AND 3 YEARS OF THE BABY'S LIFE, FOCUSING ON THE EFFECTS OF ANTIBIOTIC USE OR BIRTH PATTERNS.
In all of the above studies, the relative abundance of Bacteroides was higher in babies born vaginally than in those born by caesarean section.
Due to the lack of natural pioneer microbiota to establish microbial communities, variable community composition is thought to be driven by random rather than deterministic processes, and the effects of birth patterns on microbial community composition are still visible until the fourth year of life.
An exception to the influence of birth patterns is preterm birth, which may be due to the heavy use of antibiotics in the first days of life, characterized by unstable microbial development regardless of birth pattern. This alteration in the natural development of the baby's microbiota is associated with an increased risk of infection, immune disorders, obesity, and neuroendocrine abnormalities.
✦ Breastfeeding: Breast milk oligosaccharides bring stability to the microflora
Secondly, breastfeeding has a great impact on the development of the microbiota compared to other factors. The use of formula results in higher diversity and a more uncertain microbial community compared to breastfeeding.
For example, the lack of certain human milk oligosaccharides as the primary source of nutrients may lead to instability in initial colonization, given the natural predominance of Bifidobacterium in the gut at birth. However, the multiomic integration of microbiota, milk metabolome, and immune system development is an active and rapidly evolving area of research.
In addition to human milk oligosaccharides, human milk also contains other immunomodulatory compounds, such as lipopolysaccharides from gram-negative bacteria, secretory IgA, innate immune factors, antimicrobial peptides, and prebiotic factors.
Finally, all of these factors affect human immune development. Microbial-associated molecular pattern recognition receptors interact with microbiota-derived molecules, and metabolites such as short-chain fatty acids (which interact with GPR43, GPR41, and GPR109) and secondary bile acids (which interact with FXR) directly affect immune development.
//
Combined, these factors contribute to the formation of a distinctive, relatively stable community of bacterial, fungal, and viral microorganisms that persist for most of human life.
04
Changes in the adult microbiota
In previous sections, we have examined the dramatic changes that occur during the primary succession in infancy, compared to which the adult microbiota is largely stable (15-65 years), but the community can be disturbed, so this section discusses the following three aspects:
- Natural stable fluctuations in the microflora (circadian rhythm, diet, cleanliness, etc.)
- Disturbance of the microflora by certain factors (drugs, diseases, etc.)
- Recovery after disturbance of the microbiota
Natural steady fluctuations in the adult microbiota
The genomes of certain bacteria in healthy adults have evolved over time, suggesting that in secondary succession, functional and compositional evolution occurs in a steady state.
• Circadian rhythm influences changes in microflora
Adult microbiota also undergo natural short-term changes, with time scales ranging from one day to months or years.
A typical example of short-term variation is the circadian rhythm composed of microbial communities. Human gene expression and immune activation associated with circadian rhythms, as well as the abundance and composition of bacteria in the gut microbiota, also follow this pattern.
The family of bacteria that exhibit a diurnal cycle in mice includes Ruminococcae, Triocillaceae, Muribaculaceae, and Verrucoccaceae, but little is known about the equivalent cycle in humans.
Secondary succession in adolescence and adult life
Martino C,et al. Nat Rev Microbiol.2022
• The microbiota of the mouth and skin changes with washing
In the oral cavity, the daily amplitude of the entire group of fungi and bacteria coincides with the frequency of brushing. On the skin, fungi and bacteria also vary from day to day in line with the frequency of washing and rely on personal care products.
• Diet affects the gut microbiota
A well-studied example of a well-studied change that occurs in the range of weeks to years is diet-driven changes in the gut microbiota. Diet has a great impact on the microbial community and can include both natural and reversible changes in the community.
For example, the Hadza tribe in Tanzania consumes a diet rich in meat and tubers during the dry season, but a diet rich in honey and berries during the rainy season, showing large seasonal fluctuations in genera such as Bacteroides.
The dramatic impact of diet on microbiota formation may also play a role in human health, with much work dedicated to understanding how specific dietary components and overall dietary patterns affect the microbiota and its impact on health.
Gut bacteria prefer a lot of healthy foods like fruits, vegetables, whole grains, olive oil, etc. Studies have shown that people whose diets consist primarily of fiber-rich foods, such as the Mediterranean diet, have a greater diversity of microbiomes and are generally healthier.
In addition, for example, the Western diet is high in red meat, which is associated with all-cause mortality. The gut microbiota may convert L-carnitine, which is abundant in red meat, into trimethylamine in a harmful way, while the liver converts trimethylamine into trimethylamine nitrogen oxides, which is hypothesized to promote atherosclerosis.
The gut microbiota can also play a protective role, for example, by breaking down red meat before it is absorbed by the gut to prevent inflammation. In addition to diet, there are many other factors that contribute to the formation of the adult microbiota, including genetics, geography, host factors such as metabolic diseases, and medications.
Extended reading: In-depth analysis | inflammation, intestinal flora, and anti-inflammatory diet
The microbiota is disturbed
• Antibiotics have a huge impact on the microbiota
Secondary succession due to disruption of the microbiota has been extensively studied and examined. Among the many factors that disrupt the microbiota, antibiotics are the strongest, and recovery rates after treatment tend to vary.
The ability of the gut microbiota to rebound after antibiotic treatment is thought to depend on specific community members, such as Bacteroides and Bifidobacterium youth.
Read more: Antibiotics' effects on the microbiome and human health
Antibiotics, the natural enemies of bacteria, how to use this life-saving double-edged sword?
Disease itself can also disrupt the microbiota, whether the change is caused by a combination of factors within the microbial community, the host, or a combination of factors.
• Disease destroys the flora
——Tract: Inflammatory fungus group
Many other diseases in the intestine, such as inflammatory bowel disease, disrupt the microbial community, but do not reach a new stable community composition, but continue to be chronically unstable without intervention.
- Skin: Inflammation causes a large proliferation of Staphylococcus aureus
On the skin, atopic dermatitis is characterized by immune-mediated inflammation leading to Staphylococcus aureus blooms and reduced bacterial diversity. A decrease in the number of Malassezia species is observed during the Staphylococcus aureus overgrowth and vice versa, and the increase in the number of fungi leads to a decrease in the number of Staphylococcus aureus, which may be partly due to the ability of the fungus to produce proteases, which digest the Staphylococcus aureus biofilm and reduce the ability of the bacteria to evade the immune system.
- Oral cavity: competition and synergy between bacteria and fungi
Similar transboundary interactions exist in the oral cavity, for example, the colonization of the fungus Candida albicans relies on bacterial biofilms, but at the same time, bacterial genera such as Pseudomonas and Staphylococcus form competitive and synergistic relationships, respectively.
These examples highlight how microbial community interactions and succession are transdomain and interact with the host, but are still not fully understood due to the complex nature of their higher-order interactions.
Restoration of the microbial community
Barriers to microbial community recovery after disturbance have led many researchers to explore the possibility of targeted interventions to restore microbial communities. Microbial community restoration involves targeted reseeding or enrichment or depletion of certain species, with the aim of bringing the microbial community back to levels close to pre-disturbance.
This can be attempted with probiotics, prebiotics, antibiotics or other medications, transplantation of intact microbial complexes from healthy individuals, or a combination of these.
Although these therapies can be highly effective in restoring healthy microbial communities in certain well-characterized settings, they are often limited by a lack of mechanistic knowledge of interactions with existing communities, or by their ability to transplant only briefly.
To address these, research has focused on two areas:
The first area involves a better understanding of how communities are combined. For example, the study of human development can help determine how microbial communities aggregate during development and the effects of this aggregation later in life.
Second, new methods are being developed to identify mechanisms by exploring microbial community interactions, including computational and experimental, including high-throughput co-culture and genome editing of microbial communities.
To solve the transient problem, two main approaches are employed:
First, the transient and individualized effects of microbiota therapy are determined by the individual nature of each person's microbiota. Therefore, precision medicine targets community change to each person's unique microbiota, which has a promising future. For example, personalized nutrition based on microbial community composition was effective in improving postprandial blood glucose in a blinded randomized controlled intervention.
In addition, there is great promise for going beyond the bacterial group to explore the virome and fungal communities and the interactions between them. For example, phage therapy has been used for severe drug-resistant bacterial infections and is highly specific for targeted bacterial strains. However, most of these interventions are still in the initial research phase and are costly at scale.
05
Characteristics of the microbiota in old age
In the previous sections, we learned about the changes in the adult microbiota and the recovery after the changes, and the adult stable microbiota transforms into the final community in old age.
The exact time scale for "old age" depends on several other host-related factors, such as disease, but most of the literature to date defines "old age" as a person aged 65 years and older.
Late succession near the end of life
Aging due to biological programming and the accumulation of damage in life affects all aspects of cellular function, and the microbiota is no exception. With age, the diversity α gut microbiota decreases and β diversity increases.
There are still many unknowns about the geriatric microbiota, and while the literature is somewhat contradictory (one report reported an increase in the number of bacteroides in adults aged 65 years and older, contradicting other studies), most studies have focused on gut bacteria.
Elderly microbiota: decreased abundance of young dominant bacteria
In general, the community succession observed in the gut is a predominant and pervasive decrease in the abundance of bacteria such as Bifidobacteria, Bacteroides, Lactobacillus, and reduced resistance to opportunistic bacterial outbreaks in young adults.
•skin
In people aged 65 years and older, the number of skin bacteria in genera Cutibacterium and Staphylococcus decreased, while more Corynebacterium was observed.
•Oral
In the oral area, Rothia and Streptococcus spp. are the core oral bacterial communities, and the numbers of Porphyromonas, Treponema and Faecalibacterium spp. continue to decrease.
• Zhaodo
老年期肠道真菌群落的特征是Penicillium, Candida,Aspergillus和Saccharomyces spp.的优势度增加。
Few studies have been conducted on the skin and oral area, but the abundance of Malasseziaspp. on the skin and Candidaspp. in the oral cavity decreases.
Among intestinal phages, Siphoviridae dominates in adulthood, while Microviridae and Podoviridae dominate in old age. Compared to intestinal bacterial, fungal, and bacteriophage populations, the diversity of eukaryotic viruses remains constant after childhood and throughout the rest of life.
Research Emphasis
Due to the high degree of variability between individuals, the focus of research on microbial succession in the elderly is mainly to compare healthy and unhealthy aging.
It's unclear whether the microbiota plays a mechanical role in healthy aging or is simply a strong indicator of other variables, such as diet, exercise, and medications. However, in those who live a long and healthy life, a common denominator in the persistence of the microflora, which is highly prevalent in healthy adults, can be observed.
However, centenarians exhibit a more unique microbiome, with increased α diversity and greater inter-individual variation in community composition, complicating the comparison between "healthy" and "unhealthy" ages. Secondary bile acids are abundant in centenarians and may also play a role in healthy aging. Despite its promising prospects, this area of research is still in its infancy.
Read more: Gut microbiota and health and longevity
06
Microbial communities after death
• The succession of microorganisms does not end with the death of an individual
The death of the host can be seen as an ecological disturbance of the microbiota. Immediately after the heart stops, the tissues begin to break down due to lack of oxygen. Cellular function continues until all remaining oxygen is depleted and carbon dioxide is no longer able to transport it from the tissue. The accumulation of carbon dioxide inside the cells creates an acidic environment that is hypoxic and causes the cell to rupture.
Cellular components, such as enzymes, leak into the surrounding environment and further promote tissue breakdown in a process known as "autolysis." Autolysis triggers a series of microbial processes responsible for tissue breakdown by eliminating the immune system, loosening cellular connections, and providing nutrients to the microbiota.
The microbiota after death
Martino C,et al. Nat Rev Microbiol.2022
• Breakdown of the microbiota after death
The human microbiota is relatively stable in the first 24-48 hours after death, with different body part microbial ecology, age-α diversity patterns, and recognizable personalized skin microbiota characteristics.
In the first days to weeks of decomposition, spoilage is mainly carried out by bacteria, but as decomposition progresses, the role of the fungus increases. However, in this process, little is known about the succession and functional role of the virome.
Subsequently, environmental changes promote the succession of microorganisms, changing the human body and microbiota to no longer resemble a living individual (unless the body is frozen).
The lack of previously encountered environmental constraints in the life of the host has led to rapid changes in the relative abundance of microorganisms and their movement through various parts of the body. Migrating bacterial groups become pioneer species in the transfer from the gut to extraintestinal sites, participating in primary or secondary succession depending on the body part.
• Death microbiota – a biological indicator
The death microbiota is of increasing concern due to its impact on forensic investigations. Consistent time-series patterns associated with multiple individuals and body parts demonstrate that the postmortem microbiota can serve as a bioindicator of postmortem intervals.
The post-mortem microbiota of each cadaver is unique and varies between cadavers based on the time of death, cause of death, circumstances, place and age of death, and differences between body parts at the beginning.
When microbial succession includes rapid turnover of community members, postmortem interval estimation is more accurate in the early stages of decomposition (i.e., the first 2-3 weeks after death), but is still useful in later stages of decomposition (e.g., bones) because there is little evidence to estimate postmortem interval.
• There is a link between the cause of death and the microbiota
The link to the cause of death and the presence of the microbiota has also been demonstrated. For example, more Rothia spp. was found in the oral microbiota of individuals who died of heart disease.
In addition, skin microbiota shedding may help trace evidence by associating individuals with items they have been exposed to, however, the exact timing of this unique characteristic matching to individuals depends on the subject's material and use.
07
On sampling and experimental design in microbiota research
Study design and sample collection
The human microbiota is dynamic. With this in mind, it is important to devise a sampling strategy that captures the temporal and spatial variability of the microbiota, especially when these fluctuations are relevant to the scientific question being raised.
✦ Different measurement times: Sample collection at multiple time points
Cross-sectional studies collect one sample from each individual, while repeated measures studies collect samples at multiple time points or body parts. Over time, the sampling frequency should be adjusted to the phenomenon that the researcher is trying to observe.
For example, mouse circadian studies typically collect stool samples every 2-4 hours, while in inflammatory bowel disease, sampling patients three to five times in a week can improve disease classification.
In other applications, such as studying the effects of a particular treatment on an individual's microbiota, this may be related to conducting a "one-to-one" study in which the same participant is repeatedly tested for changes in their microbiota, and samples taken before treatment are treated as controls at the individual level.
✦ Different measurement spaces: different urban/rural environments
It is also important to consider that the microbiota of a population is highly dependent on geography and ethnicity.
For example, in a large Chinese population, a microbial that is highly age-correlated was not detected at all in a large American population.
Another concrete example relates to the "built environment" of urbanized societies, where urbanized populations are generally less exposed to environmental microbes and use household antimicrobials more, leading to significant changes compared to the human microbiota from rural societies.
These considerations are particularly relevant to the microbiota domain, as most public microbiota data come from urbanized North Americans and Europeans. As a result, the conclusions of existing datasets may not be well generalized to the global population.
Data generation
The main categories of sequencing data generated from human microbiota and microbiota studies are amplicon sequencing data and shotgun sequencing data.
✦ Amplicon sequencing
In amplicon sequencing, PCR products (amplicons) in established hypervariable regions are deeply sequenced, enabling the identification and measurement of population members by matching them to individual "barcodes".
There are two options here: which gene to amplify and which part of that gene to amplify. Common amplified regions of microbial genomes include the 16S ribosomal RNA gene of bacteria, the 18S ribosomal DNA gene of eukaryotic microorganisms, and the internal transcriptional spacer of fungi.
The choice of hypervariable regions in each specific gene depends on the specific microorganism to be captured, but the widely used hypervariable regions include the V4 region from the Earth's Microbiome Project.
✦ The intestinal microbiota is involved in the regulation of the human body
In shotgun sequencing, all microbial DNA is sequenced, not just the PCR product, enabling a more specific classification of microorganisms. Because shotgun sequencing does not rely on any marker genes, it is less biased towards certain microorganisms than amplicon sequencing.
However, shotgun sequencing is much more expensive and requires more computing power, which makes amplicon sequencing attractive without the need to increase the resolution of shotgun sequences.
Pair sequencing data with other analyses
Amplicon or metagenomic sequencing in combination with other technologies can enrich the understanding of microbiota and hosts. Techniques such as quantitative PCR and fluorescence-activated cell sorting provide additional context for relative abundance by anchoring relative abundance to reliable absolute abundance measurements.
Enzyme-linked immunosorbent assays and single-cell sequencing can be well paired with metagenomic sequencing by providing host cell type or host immunity information.
Cultureomics enables researchers to experimentally verify genomic predictions of function or activity and convert microorganisms into probiotics. Metabolites or proteins produced by microorganisms, i.e., downstream effectors of the microbiota, can be probed by metabolomics and proteomics, respectively.
Finally, host genomics and transcriptomics are increasingly paired with amplicon or metagenomics data to gain insight into the link between host gene expression and microbiota.
Metadata collection
Finally, it is crucial to collect data from the participants being surveyed. Some important metadata categories for general microbiota studies include demographic, clinical, and dietary information; however, the exact metadata used varies from study to study. Practices that produce standardized metadata should be adopted so that results can be reused and reproducible.
Conclusions and prospects
This article describes the current state of research on the composition of the human resident microbial community at different ages and on different body parts.
There are many links between human health and microbiota composition, and interventions in the gut microbiota may improve health. Interventions that focus on the enrichment or elimination of entire microbiota rather than individual species require an understanding of how these communities are formed and maintained.
The microbiota of different populations and different parts of the population needs to rely on the construction of a large sample database, which provides a guarantee for the accuracy of microbiota research.
By studying the microbiota throughout the human lifespan, we can better understand the complex interactions of these microbiota and how to effectively push the microbiota to the components needed to the host. It is also being applied in other fields besides human health, such as forensic science. With the continuous breakthrough of microbiota related research, it will have a huge impact on human life, health and production and life.
Featured References
Martino C, Dilmore AH, Burcham ZM, Metcalf JL, Jeste D, Knight R. Microbiota succession throughout life from the cradle to the grave. Nat Rev Microbiol. 2022 Jul 29. doi: 10.1038/s41579-022-00768-z. Epub ahead of print. PMID: 35906422.
Lim, A. I. et al. Prenatal maternal infection promotes tissue-specific immunity and inflammation in offspring. Science 373, eabf3002.
Al Nabhani, Z. & Eberl, G. Imprinting of the immune system by the microbiota early in life. Mucosal Immunol. 13, 183–189.
Helve, O. et al. 2843. Maternal fecal transplantation to infants born by cesarean section: safety and feasibility. Open. Forum Infect. Dis. 6, S68.
Seppo, A. E. et al. Infant gut microbiome is enriched with Bifidobacterium longum ssp. infantis in old order mennonites with traditional farming lifestyle. Allergy 76, 3489–3503.