So the human metagenomic microbiota will not survive when transfected into a mouse. If you take the human microbiotaThe bacterial community in the human body. Many species in the microbiota contribute to the development of chronic disease, put it into a mouse, the mouse will be able to deal with it because, it’s VDR isn’t really as important as man’s is.

  • REVIEWMetagenomic Surveys of Gut Microbiota
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New insights in gut microbiota and mucosal immunity of the small intestine

The causes of obesity are incredibly broad, but one 2009 study may suggest a cause that begins in the oral microbiome. In over 98% of the women with obesity studied, the bacteria Selenomonas noxia was found in very high levels in saliva compared to the control group.


Tiny microbes, enormous impacts: what matters in gut microbiome studies

This finding suggests that there exists a niche in the human gut for metabolizing uronic acids (a class of sugars derived from proteoglycans) that is differentially filled by distinct subsets of each individual’s microbiome. Like ribosomal protein- and chaperone-coding genes, genes involved in uronic acid metabolism were also found to be variably transcribed across subjects, perhaps because of variation in the subject’s dietary patterns.

Gut microbiota lipopolysaccharide accelerates inflamm-aging in mice

This signal can be explained predominantly by the presence of the archaeon Methanobrevibacter smithii in five of the eight HPFS subjects. In these five subjects, the relative abundance of M. smithii at the DNA level ranged from 0/005 to 0/053 (0/5–5/3%), whereas its relative contribution to the pool of species-specific transcripts ranged from 0/021 to 0/147 (2/1–14/7%) (SI Appendix, Fig.


Prebiotic supplementation in frail older people affects specific gut microbiota

Olsen, I, & Yamazaki, K. (2021). Can oral bacteria affect the microbiome of the gut. Journal of oral microbiology, 11(1), 1586422.

Bergersen, F. J. & Hipsley, E. H. The presence of N2-fixing bacteria in the intestines of man and animals. J Gen Microbiol60, 61–65 (1970).


The gut microbiota of rural Papua New Guineans: composition, diversity patterns, and ecological processes

Fresh feces were collected from each subject on the day of examination by independent defecation or via digital rectal examination. Each sample of fresh feces (5 g) was labeled and preserved in 2 mL of RNAlater Stabilization Solution (Sigma) and transported using dry ice. On arrival at the laboratory all fecal samples were stored at −80°C until further use (Anderson et al, 2021; Claesson et al, 2021; Vogtmann et al, 2021).

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Normann, E, Fahlen, A, Engstrand, L, and Lilja, H. E. (2021). Intestinal microbial profiles in extremely preterm infants with and without necrotizing enterocolitis.

As 70%+ of your immune system is located in your gut, it’s no shock that the gut microbiome plays a big part in immunity. However, immunity actually begins in the mouth, the headwater to the entire digestive system.


What is the oral microbiome

Use this process to fulfil their nitrogen demands. For example, the microbiota associated with invertebrates living in nitrogen-poor environments occasionally include diazotrophs (nitrogen-fixing prokaryotes).

Diversity of the gut microbiota and eczema in early life

The tongue is sometimes forgotten in the course of dental hygiene habits. However, there’s a simple solution: start tongue scraping.


The age-related changes in microbiota composition have been shown to play a role in development of neurodegenerative disorders, including Parkinson’s disease (PD) and Alzheimer’s disease (AD). For example, Akkermansia muciniphila, which is the only known bacterial species of phylum Verrucomicrobia is generally recognized as a probiotic. Supplementation of this species was shown to restore the integrity of epithelial mucosa, reduce weight gain, improve glucose tolerance, and alleviate metabolic endotoxemia and inflammation in animal models of diabetes and obesity (Vaiserman et al, 2021). In our study, we observed a declining trend in the abundance of Akkermansia muciniphila in centenarians. These results are in keeping with the metabolic disorders that ensue with changes in physical state before death.

Comparison of Oral-Gut Microbial Ecology in the HPFS and Human Micobiome Project Cohorts

That’s why 6-month teeth cleanings are important to keeping your oral microbiome healthy. The plaque buildup your hygienist removes can otherwise contribute to the dysbiotic growth of pathogenic oral bacteria.


Members of the Clostridiales and Bacteroidales (Figs 2a and 3), L. multipara ATCC 19207, Ruminococcaceae bacterium AE2021, and P. bryantii B14 lack His422 in NifD, but all the essential cysteine residues are conserved, as in E. proavitum. The other members of Clostridiales in this clade retain both the histidine and cysteine resi-dues. In the NifD homologues recovered from the human faecal metagenomes (next page), both of those with and without the histidine residue were identified. None of the NifD homologues lacked the cysteine residues. Therefore, there is currently no reason to consider that these bacteria cannot fix dinitrogen.

For RNA-seq libraries, 5 μg of initial RNA was depleted for ribosomal RNA using Ribo-Zero (Epicentre), subjected to DNase treatment to deplete remaining sample DNA, fragmented, and then used as a template for strand-specific cDNA synthesis by dUTP marking and degradation of second strand cDNA (35). This procedure has been known to introduce 1–2% Escherichia coli genomic DNA into the final cDNA library (a result of E. coli-derived DNA polymerase I and ligase being used in the cDNA generation steps). Including versus excluding E. coli sequences in downstream bioinformatic analyses did not affect the conclusions of this work. RIN scores for all metatranscriptomic samples are provided in SI Appendix, Table S1. The average RIN score over all samples was 6/9, whereas the averages for the control, EtOH-fixed, RNAlater-fixed batches were 5/7, 7/0, and 7/8, respectively.

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The gut-brain axis is a well-established part of scientific theory. From depression to Alzheimer’s, a healthy gut biome is integral to decreasing your risk for diseases of the brain and nervous system.


When applying MetaPhlAn to RNA read data, the output is a profile of relative marker gene transcription across clades (focusing on species-level measurements in this work). A species’ value in this profile depends on two factors: (i) its overall genomic abundance in the sample, and (ii) the average transcriptional level of its unique marker genes. Notably, only the first criterion matters when quantifying species abundance at the DNA level, as each marker gene is expected to occur at equal frequency after normalization. If a species has higher RNA-based abundance than DNA-based abundance, this suggests that its marker genes are more actively transcribed than marker genes from other species, which we can interpret as an approximate measure of the species’ clade-specific transcriptional activity.

After the first round of multidisciplinary physical examination, the dominant gut microbiota at genus and species level in healthy Hainan centenarians exhibited significant differences from those of centenarians in the Mediterranean diet area of northern Italy (Figures 3, 4) (Collino et al, 2021). However, it is not clear whether the differences were associated with MEDI-LITE.


Butyrivibrio species, of which NifH sequences constitute a clade with those from the human faecal microbiota

Upon receipt at the laboratory, saliva tubes were frozen to −80 °C. The stool samples were homogenized using a spatula and separated into three aliquots (fresh-frozen control, mock-shipped RNAlater-fixed, and mock-shipped ethanol-fixed). The homogenization step was intended to reduce between-aliquot variability for the purposes of our methods evaluation; subjects using the self-collection and self-shipping protocol validated here would not be required to homogenize their stool. The first 100-mg subsample (control) was flash-frozen on dry ice and then stored at −80 °C until being thawed for extraction. The control aliquot represented the baseline composition of the sample upon arrival at the laboratory, following the initial HMP-based sample collection and transport protocol described above. To a second 100-mg subsample we added 700 μL of RNAlater (Ambion) and then allowed the mixture to fix at −4 °C overnight. A third 1-g subsample was collected using a feces tube with spatula (catalog 80/623/022, Sarstedt), to which we added 5 mL of 95% (wt/wt) ethanol and allowed the mixture to fix at room temperature overnight. The stool masses described above were acquired by taking a single scoop with a corresponding collection spatula, just as subjects would do when following the proposed self-collection protocol. Ethanol- and RNAlater-fixed subsamples were then stored at −80 °C until all samples were ready for the mock-shipping stage of the experiment. During mock-shipping, all ethanol- and RNA-later fixed samples were transferred to a cardboard box and subjected to natural environmental condition changes (at ambient temperatures) for 48 h to mimic conditions during carrier or mail transport. After this phase, mock-shipped samples were then stored at −80 °C until extraction; the frozen control and RNAlater-fixed subsamples entered the extraction pipeline directly, whereas the ethanol-fixed subsamples were first sliced to yield 100 mg of stool.

Combined with a mixture of 600 μ l of the RLT buffer contained in the kit, 7 μ l of β -mercaptoethanol, 100 μ l of TE buffer, and 300 mg of glass beads, and disrupted with the Shakemaster Auto for 5 min. The subsequent pro-cedure was performed according to the manufacturer’s guidelines. DNA was removed from the extracted RNA with the Turbo DNA-free Kit (Ambion) at 37 °C for 1 h. Reverse transcription was performed at 55 °C using the SuperScript III First Strand Synthesis System (Invitrogen) with 0/5 μ M nifH3 primer23.


I’ve mentioned it once already, but a dry mouth is a perfect home for bacterial overgrowth. In fact, I think it might be a bigger contributor to cavities, gum disease, and bad breath than even diet!

The oral microbiome is a major player in the mouth-body connection. Sadly, many approaches to dental care don’t consider how important it is to support a healthy flora within the mouth. Instead, we’re told to disinfect, sanitize, and “clean” the mouth.


While C-section is necessary in some cases and can be a great thing for risky deliveries, missing out on the biome is a big deal. It’s known to contribute to the risk for gut and overall health issues including celiac disease, asthma, type 1 diabetes, and obesity. In fact, Slackia exigua, one oral pathogen, is found exclusively in C-section delivered babies.

Figure 2. The abscissa represents the grouping of samples, and the ordinate represents the number index of species under different grouping. The external shape is the density distribution, and the internal black spot represents the position of the sample. Asterisk (*) indicates significant difference (0/01 < P < 0/05); double asterisk (**) indicates extremely significant difference (P < 0/01); NS indicates no significant difference.


Diverse and abundant sequences were assigned to Cluster IV, which is also called the ‘NifH-like cluster’. The function of Cluster IV NifH is largely unknown, but it has been suggested to play a role other than in nitrogen fix-ation24,26.

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Standard curves were constructed in triplicate using serial dilutions of linearized plasmids containing each target sequence. Quantitative PCR amplification was performed with the FastStart Essential DNA Probes Master (Roche Diagnostics) on the LightCycler Nano System (Roche) under cycling conditions: 95 °C for 10 min, and 40 cycles of 95 °C for 10 s and 60 °C for 30 s. Specific amplification was verified by cloning and sequencing the PCR products.

Description of Metagenomic Analysis

Data pertaining to 191 fecal samples from 75 Hainan healthy centenarians were included in the dynamic cohort analysis (centenarians died at different times, therefore not all of them could successfully collect five samples; only 191 stool samples were collected in total). All participants were determined to be healthy centenarians by multidisciplinary examination and had resided in the Hainan Province for more than 20 years (average age: 103/1 ± 2/8 years). Fifty-nine (78/7%) centenarians were female. The follow-up survey lasted for 20 months; 20 participants died during this period, the median survival time was approximately 8–9 months, and the one-year mortality rate was 14/7%. By comparing the health status scores, we found that the median time of significant decline in the physical condition of the subjects was about 3 months. All subjects died at their home in this study due to the scattered residence. All centenarians who participated in the survey received financial subsidy from the local civil affairs, which was paid by a specially designated person on a monthly basis. Moreover, it was checked whether the old people were still alive; therefore, the timing of deaths were available for all subjects. However, no official death certificate was available for all subjects. The follow-up survey indicated that the main symptoms of the centenarians before death were anorexia and reduced dietary intake.


In the mouth, frequent sugar intake moves the pH in the mouth to be more acidic. An acidic environment contributes to the demineralization of teeth.

Morita, A. et al. Development, validation, and use of a semi-quantitative food frequency questionnaire for assessing protein intake in Papua New Guinean Highlanders. Am J Hum Biol27, 349–357 (2021).


DNA was extracted from each fecal sample using improved protocol based on the manual of QIAamp Fast DNA Stool Mini Kit (Qiagen, Germany). In detail, 1 mL of InhibitEX Buffer and adequate amount of glass beads (0/5 mm diameter, Qiagen) were added to each 200 mg of feces. The mixture was homogenized twice with a Homogeneous instrument (FASTPREP-24, Aosheng Biotech, China) for I min each at a frequency of 60 Hz. Subsequently, DNA purification was performed according to the manufacturer’s instructions. DNA paired-end libraries with an insert size of 500 bp were prepared following the Illumina TruSeq DNA Sample Prep v2 Guide (Illumina, Inc, San Diego, CA, United States). Quality of all libraries was evaluated using an Agilent bioanalyzer (Agilent Technologies, Wokingham, United Kingdom) and the DNA LabChip 1,000 kit. All samples were subject to 150 bp paired-end sequencing using an Illumina HiSeq 2500 sequencer (Illumina, Inc, San Diego, CA, United States).

The human gastrointestinal tract is home to immense and complex populations of microorganisms. Using recent technical innovations, the diversity present in this human (https://aprel-vologda.ru/hack/?patch=8142) body habitat is now being analyzed in detail. This review focuses on the microbial ecology of the gut in inflammatory bowel diseases and on how recent studies provide an impetus for using carefully designed, comparative metagenomic approaches to delve into the structure and activities of the gut microbial community and its interrelationship with the immune system.


Saez-Almendros, S, Obrador, B, Bach-Faig, A, and Serra-Majem, L. (2021). Environmental footprints of Mediterranean versus Western dietary patterns: beyond the health benefits of the Mediterranean diet.

In addition to validating methods for microbiome sample collection, to our knowledge this work represents one of the first efforts to probe the functional activity of the human (https://aprel-vologda.ru/hack/?patch=1705) gut microbiome via combined metagenomic and metatranscriptomic sequencing. This approach produced the striking finding that more than half of the variation in microbial community gene expression can be explained by metagenomic composition (Spearman’s r = 0/76; r2 = 0/58 = 58%). In other words, a gene family’s copy number in the community appears to be the (slightly) dominant determinant of the abundance of its corresponding transcript. Microbial gene expression is no doubt influenced by many other factors, such as variation in the gene’s promoter strength across genomes (strains) and the regulatory states of cells within and across species. However, our results indicate that these factors are on par with genome content in dictating the metatranscriptome composition of the healthy human gut. Notably, our observation of strong correlation between metagenomic and metatranscriptomic composition is consistent with the majority of genes across the majority of microbial genomes being transcribed at similar, relatively fixed rates, a reasonable null model for a community of single-celled organisms well-adapted to their environment. Significant deviations from this model are indicative of finer-level transcriptional control occurring within the microbiome, and can be divided into two types, both of which were observed in this study: (i) consistent up- or down-regulation of a function across individuals, and (ii) regulation that varies in a subject-specific manner.


Visceral pain: gut microbiota, a new hope

Relative abundance values were arcsine square root-transformed before performing ANOVA calculations to variance-stabilize data and better approximate normality. Before computing the RNA/DNA abundance log ratios and RNA- and DNA-level coefficients of variation, all KO-based relative abundance measurements for a sample were smoothed by the Witten–Bell method (39). This procedure calculates the probability mass likely to have been nonobserved because of low frequency events and evenly distributes it over all nonobserved genes in each sample. This method can in many cases provide an accurate way to avoid numerical irregularities, such as dividing a small RNA abundance by zero DNA abundance. The size of the additional probability mass is equal to the number of “first observations” over all detected KOs divided by the total number of observations, which is approximated as the reciprocal of the smallest nonzero relative abundance. This procedure was only applied to genes detected with a relative abundance of at least 10−4 (0/01%) in at least one sample.

Red circles correspond to KOs where RNA > DNA; blue circles correspond to KOs where DNA > RNA. Marks on the x or y axis margins represent KOs with zero measured abundance in one dataset but nonzero abundance in the other. The trends illustrated here were all of large effect (fold-change > 2) and statistically significant following FDR correction (Methods).


Early high-throughput metatranscriptomic investigations of microbial communities were focused largely on ocean-derived environmental samples (4⇓–6). These efforts demonstrated the feasibility of RNA-based profiling of microbial community structure, function, and diversity, and also produced large amounts of novel sequence information (transcripts) unseen by earlier metagenomic investigations. Metatranscriptomic analysis has subsequently been applied to the human (see) gut microbiome, revealing strong intersubject and temporal variability in microbial gene expression, as well as core modules of actively transcribed versus repressed functions (7⇓–9). In addition, metatranscriptomic analyses of the gut microbiome during exposure to dietary (10) and xenobiotic (2) interventions have revealed significant alterations of the microbial community gene-expression profile, but often without large changes in overall community structure. One of the next major challenges facing human (https://aprel-vologda.ru/hack/?patch=2568) microbiome studies is relating the current understanding of microbial ecology to this growing knowledge of the biomolecular activities and regulatory systems of the microbiota (continue) (11).

In the mouth and body, nitric oxide is a vital nutrient to support the body’s natural repair processes. It’s involved in systems from the gut to the brain and can improve blood pressure, digestion, cancer risk, chronic inflammation, sleep, endurance, and insulin resistance.


There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.

Alterations of the human gut microbiome in liver cirrhosis

Like leaky gut, this permeability in the mouth is closely connected to the ability of bacteria to make their way past the gums into the rest of the body. It’s been most studied in conjunction with diabetes, a disease known to run in tandem with chronic periodontitis.


Microarray-based genomic selections for gut microbiome sequencing were carried out using Hiseq2500; about 13/44 ± 3/82 Gb data was obtained from each sample on average. Moreover, phenotypic information of these centenarians were collected on the first round, including dietary and living habits, past medication history, and information from multidisciplinary health examination. Through quality control and removal of sequence reads mapping to the human genome by using MetaPhlAn 2/0, the results of microbiome sequencing were mapped to about 1 million genes of microbial taxonomic specific marker to predict the relative abundance of different microbiota (https://aprel-vologda.ru/hack/?patch=7035). For each participant, we predicted abundance of 1,361 microbial taxonomic clades, ranging from four phyla to 534 species. Most of the reads were from bacteria (97/96%), 0/22% were from archaea, 1/81% were from viruses, and the last 7/55e-05% pertained to eukaryotes. Bacteroidetes and Firmicutes were the two dominant phyla at the phyla level, while Escherichia and Bacteroides were the two dominant genera at the genus level (Escherichia coli and Prevotella copri at the species level). The fecal metagenome (https://aprel-vologda.ru/hack/?patch=7297) of 191 longevity individuals was sequenced using Illumina platform. Finally, 6,655,439 microbial genes were obtained, with an average length of 682 bps.

Rand, W. M, Pellett, P. L. & Young, V. R. Meta-analysis of nitrogen balance studies for estimating protein requirements in healthy adults. Am J Clin Nutr77, 109–127 (2003).


Drink soda, fruit juices, coffee, kombucha, or alcohol over long periods of time. While coffee and kombucha offer some health benefits, sipping on these throughout the day contributes to demineralization. If you’re going for one of these beverages, try keeping it to 20-30 minutes, then brushing about 30-45 minutes afterwards.

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Candidiasis of the mouth (oral thrush) is another sugar-related symptom of a systemic issue with sugar. In the gut as well as the oral cavity, Candida overgrowth is best treated with a multi-system approach that always includes cutting out sugar, and includes other treatments like glutamine rinse, chewable CoQ10, and vitamins and minerals to promote immune function.

Zehr, J. P. & McReynolds, L. A. Use of degenerate oligonucleotides for amplification of the nifH gene from the marine cyanobacterium Trichodesmium thiebautii. Appl Environ Microbiol55, 2522–2526 (1989).


The taxonomic profiles of these species were compared with stool and tongue samples from the HMP cohort, with tongue representing the oral community. Samples were clustered by Bray–Curtis distance, and species were clustered by rank correlation. Note that samples cluster strongly by body site (oral vs. gut). Highly abundant oral species are more likely to be detected at low levels in the gut. Green numbers associate oral-gut co-occurring species with detailed abundance profiles in B and C. (B) Eight abundant oral species detected in the HPFS saliva samples were detectable at low abundance in the stool samples from the same individuals, but showed minimal transcriptional activity in the stool.

OTU-08 was recovered as both genes and transcripts from a PNG faecal sample. This OTU shared 98% amino acid sequence identity with NifH of Lachnospira multipara and also 97% identity with those of Butyrivibrio species and Ruminococcaceae bacterium AE2021. These bacteria have been isolated from ruminant foreguts, according to the description in the sequence database. OTU-34 was recovered as gene clones from two PNG samples. This OTU shared more than 97% amino acid sequence identity with NifH of Lachnospiraceae bacterium 3-1 isolated from a mouse cecum and Ruminococcaceae bacterium AE2021 and Prevotella bryantii isolated from ruminant foreguts.


The Human Gut Microbiota: Toward an Ecology of Disease

Of 95% nucleotide sequence identity. The NifD and NifK sequences were identified with BLASTP using a cut-off of E-value ≤ 10–5 against NifD (K02586) and NifK (K02591) in the KEGG database, respectively.

Gut microbiome-host interactions in health and disease

Headlines plaster the importance of gut health on every major health-related website. The gut is central to human (https://aprel-vologda.ru/hack/?patch=8463) health, and at its core, gut health is determined by the diversity and population of the gut microbiome (also known as gut microbiota or gut flora).


Zehr, J. P, Jenkins, B. D, Short, S. M. & Steward, G. F. Nitrogenase gene diversity and microbial community structure: a cross-system comparison. Environ Microbiol5, 539–554 (2003).

Key Takeaways: The Oral Microbiome

This has established the importance of the gut microbiome in the disease pathogenesis for numerous systemic disease states, such as obesity and cardiovascular disease, and in intestinal conditions, such as inflammatory bowel disease. Thus, understanding microbiome activity is essential to the development of future personalized strategies of healthcare, as well as potentially providing new targets for drug development. Here, we review recent metagenomic (https://aprel-vologda.ru/hack/?patch=2349) and metabonomic approaches that have enabled advances in understanding gut microbiome activity in relation to human health, and gut microbial modulation for the treatment of disease. We also describe possible avenues of research in this rapidly growing field with respect to future personalized healthcare strategies.


Deo, P. N, & Deshmukh, R. (2021). Oral microbiome: Unveiling the fundamentals. Journal of oral and maxillofacial pathology: JOMFP, 23(1), 122.

Metaproteomic analysis of human gut microbiota: where are we heading

Recently, gingival bacteria has earned the public eye as a potential cause of Alzheimer’s disease. A groundbreaking study released in early 2021 proposed a rare causative link (not just a correlation) between the bacteria most responsible for gum disease and Alzheimer’s disease in the brain. For years, researchers have understood there was a connection between these two conditions, but not much about how or why this was the case.


Gut microbiota community and its assembly associated with age and diet in chinese centenarians

This work is licensed under a Creative Commons Attribution 4/0 International License. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material.

However, whether the gut microbiota truly has this potential remains unclear

In a more acidic environment, S. mutans and yeast take over, eventually causing dental caries. While the literature doesn’t use the term “dysbiosis” in regards to oral health, the microbial imbalance in the mouth that triggers the development of dental caries certainly qualifies as dysbiosis.


Given that the vast majority of gut-dwelling bacteria are anaerobic (26), the observed overexpression of the citrate cycle is best explained by its role in replenishing biochemical intermediates, rather than its role in aerobic metabolism. This finding is consistent with the observation that only genes involved in one part of the cycle (reactions yielding oxaloacetate) were significantly overexpressed and emphasizes the need to avoid the blind application of broad pathway names to specific biochemical functions observed in the microbiome.

Technology Advancement Enabling the Link of Gut Microbiota with Obesity and Metabolic Disorder

Several hundred species of bacteria (700+ identified at the time of this writing) exist within this delicately balanced colony. The most prevalent of these are also found in the other three biomes in smaller numbers. This balance of bacteria in the oral cavity is the second most diverse biome of the body, second only to the gut.


There are many interactions that may lead to IBD, like genetics and epigenetics, immune responses, and bacterial imbalances. However, one such factor that’s gained more attention in recent years is the connection between IBD and oral disease.

Metagenomics: key to human gut microbiota

We observed many examples of gene families that were metagenomically abundant but consistently down-regulated at the transcriptional level. The relative functional importance of such genes to the healthy human gut will tend to be overestimated by metagenomics-only approaches. However, the fact that such functions persist in the gut microbial community’s reservoir of functional potential suggests that they are selectively advantageous under conditions not captured by this study. For example, although sporulation was inactivated in these healthy subjects with, presumably, a fully populated spore component, this pathway persists as a survival mechanism to be activated in response to stress, starvation, or perturbation of the existing spore population (as might occur subsequent to antibiotic treatment). Conversely, a small number of functional modules were consistently transcriptionally activated well beyond their metagenomic abundance, and will tend to be underestimated by metagenomics-only approaches. This was particularly the case for methanogenesis, which demonstrated transcriptional abundance one-to-two orders-of-magnitude greater than its metagenomic abundance.


Zou, Q. H, & Li, R. Q. (2021). Helicobacter pylori in the oral cavity and gastric mucosa: a meta‐analysis. Journal of Oral Pathology & Medicine, 40(4), 317-324.

We found that the inflection point of significant changes in gut microbiota was 7 months before death

The first round of centenarians’ survey included questionnaire for baseline survey, collection of biological specimens, and physical and laboratory examination. The questionnaire survey was conducted by nurses who were conversant with the Hainan dialect.


As a dentist, I was taught all about how the bacteria in the mouth cause oral disease. From gingivitis to candida/oral thrush to cavities, an overabundance of pathogenic (disease-causing) bacteria can cause a slew of problems.

Relating the metatranscriptome and metagenome of the human gut

Spearman’s rank correlation: ρ= 0/21). The acetylene reduction assay supported the occurrence of nitrogen fixa-tion in the two Japanese samples with high nitrogen intake (209/1 and 183/2 mg/kg body weight/day). The emis-sion of ethylene was observed in the presence of acetylene (Supplementary Figure S1), and the nitrogen fixation rates were estimated to be 0/008 and 0/143 nmol/g/h, when the theoretical reduction ratio C2H2:N2≈ 322 was used.


A frozen faecal sample was treated with 15 mg/ml lysozyme at 37 °C for 1 h, with 60 units/ml purified achro-mopeptidase (Wako 015-09951, Japan) at 37 °C for 30 min, and then with 1% SDS and 1 mg/ml proteinase K at 55 °C for 1 h. The sample was subjected to phenol/chloroform/isoamyl alcohol extraction and isopropanol pre-cipitation. The extracted DNA was treated with RNase A, and purified with polyethylene glycol precipitation to remove any residual protein. The purified DNA was suspended in 300 μ l of TE.

Foster, J. A, & Neufeld, K. A. M. (2021). Gut–brain axis: how the microbiome influences anxiety and depression. Trends in neurosciences, 36(5), 305-312.


Infant gut microbiota and the hygiene hypothesis of allergic disease: impact of

From this study, we can’t determine a cause-and-effect. For instance, the dietary patterns in many obese people dysregulate the oral microbiome because they’re so high in starchy carbohydrates and sugar.

Through ageing, and beyond: gut microbiota and inflammatory status in seniors and centenarians

I’ll get to dietary ways to support the oral biome below, but first: Oral infection can cause major issues within the rest of the body in a variety of ways. These include bacteremia (escape of bacteria through the gums to the bloodstream), system-wide inflammation, and infection of bacterial toxins that make their way throughout the body.


This study showed significant differences in gut microbiota among centenarians in different areas

Proper immune response is one way your body keeps a handle on normal inflammatory processes. Pathogens in the oral cavity can overthrow this delicate balance and create chronic inflammation.

Beyond your birth and breastfeeding history, there are several ways to support the health of your oral microbiome. By extension, this can help make your entire body healthier!


Nitro-gen intake was determined with Pearson’s product–moment correlation coefficient (r) and Spearman’s rank cor-relation coefficient (ρ). The calculation of the 15N mass is shown in Supplementary Table S1.

Mohamed, N. M, Colman, A. S, Tal, Y. & Hill, R. T. Diversity and expression of nitrogen fixation genes in bacterial symbionts of marine sponges. Environ Microbiol10, 2910–2921 (2008).


Knomics-Biota - a system for exploratory analysis of human gut microbiota data

This condition is intrinsically linked to the quality of the gut microbiome. A high prevalence of Prevotella bacteria, in particular, is implicated in polycystic ovarian syndrome.

Richness of human gut microbiome correlates with metabolic markers

Hardy, R. W, Holsten, R. D, Jackson, E. K. & Burns, R. C. The acetylene-ethylene assay for N2 fixation: laboratory and field evaluation. Plant Physiol43, 1185–1207 (1968).


Instances of HIV/AIDS may also be affected by oral microbiome health. There is evidence that biome diversity in the mouth is much different in unmanaged HIV/AIDS than in healthy controls.

Nitro-gen and balance between nitronitro-gen fixation and nitrification have been suggested to explain these examples. In another case, certain plant-associated diazotrophs are less sensitive to ammonia in the symbiotic phase than in the free-living phase, and contribute to the nutrition of the host1.