Your trusted health, nutrition, and personalized lifestyle medicine resource

Meal Timing Impacts Daily Rhythms of Human Salivary Microbiota

The digestive system begins in the mouth

by Ashley Jordan Ferira, PhD, RDN

The digestive system begins in the mouth, which is home to 700+ unique species of bacteria.1 Research has shown that salivary2 and gastrointestinal (GI)3-4 microbiota possess diurnal rhythms; whether these daily patterns are a result of circadian biology and/or eating behaviors is unknown. The composition of one’s habitual diet has been shown to impact human GI microbiota, and emerging research suggests that eating frequency and timing of meals may also play a role,3-4 however, longitudinal human interventions are needed to understand the clinical relevance of microbial changes.

The “what” and “when” of meals also have implications for metabolic dysfunction and obesity. Honing in on the “when” variable: meal timing, in particular consuming one’s main meal later in the day, has been linked to insulin resistance4 and less weight loss.6 Caloric distribution, specifically eating a high calorie breakfast (vs. high caloric dinner) is associated with improvements in insulin resistance.7 Mechanisms underlying late eating-induced metabolic dysfunction are not well understood, but salivary and gut microbiota composition have been associated with obesity8-9 and metabolic perturbations.10 Could meal timing affect metabolic dysfunction and obesity via changes in gut microbiota?

An international collaboration of researchers published the first human intervention to investigate the impact of meal timing on digestive tract microbiota (in saliva and feces), specifically examining whether eating late affects daily rhythms of salivary microbiota.11 They implemented a randomized, crossover study in 10 healthy (normal BMI) women (average age: 25) from Spain. The 2 meal timing experimental periods (7-day duration each) included:11

  • Early eating (EE) – lunch at 2pm
  • Late eating (LE) – lunch at 5:30pm

* Note: timing of breakfast (8:30am) and dinner (9pm) were fixed during EE and LE, with no snacks allowed

* Note: 7-day washout period between EE and LE, in which participants ate meals at usual times (e.g. average usual lunch time was 2:33pm)

During the EE and LE experimental periods, all participants were provided the same, controlled diet with 3 standardized meals (breakfast, lunch, dinner) designed to provide sufficient energy for weight maintenance. During the 2 experimental weeks (EE and LE):11

  • Average calories: 1868 kcal/day, supplied via 50% carb, 35% fat, and 15% protein
  • Average fiber intake: 30 g/day
  • Daily energy distribution: 26% from breakfast, 47% from lunch, 27% from dinner

Usual sleep patterns were maintained. Anthropometry (height, weight, waist circumference) and total body fat (via bioelectrical impedance) were measured. Salivary sample collections occurred on day 0 (baseline), day 7 (last day of either EE or LE intervention), day 14 (washout), and day 21 (last day of either EE or LE intervention). Fecal samples were collected on day 7 and 21. No food or beverage were allowed within 1 hour of saliva sampling, and no toothpaste was allowed within 24 hours of saliva collections. To assess the salivary microbial daily rhythm over a 24-hour period, serial saliva samplings on day 7 and 21 occurred at:11

  • Wake time -> wake time + 4h -> wake time + 8h -> wake time + 12 h

* For example, for an 8am waking time: samples were taken at 8am, 12pm, 4pm, and 12am

Microbiota profiling and analyses were used to assess changes in microbial community structure. No significant differences were seen in fecal microbiota composition or structure between LE and EE conditions, however trends were seen for higher abundance of Fusobacteriaceae and Peptostreptococcaceae families for the LE and EE conditions, respectively.11 The following findings are for salivary microbiota:11

  • In all samples, the most abundant genera were Streptococcus, within the Firmicutes phylum
  • There were no differences in relative abundance of individual bacteria at any taxonomic level between LE vs. EE at any time of the day
  • For both EE and LE, daily rhythms were observed for salivary microbiota diversity and abundance
    • Specifically, significant daily rhythms were observed in phylum level Fusobacteria for LE and in TM7 for EE
  • Meal timing impacted daily rhythms of salivary microbiota diversity
    • Specifically, LE inverted the daily rhythm (toward opposite pattern than EE), with higher microbial diversity during the middle of the day
  • LE, but not EE, increased the relative abundance of salivary bacterial taxa thought to be pro-inflammatory pathobionts (i.e., Fusobacteria genera Leptotrichia sulfate-reducing bacteria and Bacteroidetes genus Porphyromonas and Prevotella)

This well-designed randomized, crossover study showed that daily rhythms exist in human salivary microbiota, and for the first time, that meal timing impacts daily rhythms of human salivary microbial diversity and abundance, even in healthy young women with no metabolic dysfunction.11 Eating the main meal late in the day (even just for 1 week) appeared to invert the daily rhythm of salivary microbiota diversity; the study authors posit that the higher microbial diversity during the middle of the day caused by LE and the increased relative abundance of pro-inflammatory bacteria observed share microbial patterns previously observed in obesity and inflammation.11-12

This study provides rationale for future research on human oral and gut microbial rhythms to understand the relationship between food timing and metabolic alterations. It should be noted that lunch is the main meal of the day in many European countries (including Spain, where this study was conducted). It would, therefore, be edifying for future studies to investigate the impact of main-meal-timing for dinner (e.g. representative pattern for many in the US), or the differential impact of a large vs. small breakfast.

Why is this Clinically Relevant?

  • Metabolic syndrome and obesity are common in developed countries, and research is needed to elucidate the role the human gut microbiota plays in metabolic disorders8-9
  • Meal timing, particularly eating later in the day, has been previously linked to insulin resistance and obesity5-7
  • In the first human study of its kind, meal timing (late eating) was seen to affect the daily rhythms of salivary microbiota11
  • Additional human studies are needed to understand how food timing and perturbations in oral or GI microbiota impact health and disease

Link to abstract


  1. Kilian M, Chapple ILC, Hannig M, et al. The oral microbiome- an update for oral healthcare professionals. BDJ. 2016;221:657-666.
  2. Takayasu L, Suda W, Takanashi K,e t al. Circadian oscillations of microbial and functional composition in the human salivary microbiome. DNA Res. 2017;24(3):261-270.
  3. Kaczmarek JL, Musaad SM, Holscher HD. Time of day and eating behaviors are associated with the composition and function of the human gastrointestinal microbiota. Am J Clin Nutr. 2017;106(5):1220-1231.
  4. Kaczmarek JL, Thompson SV, Holscher HD. Complelx interactions of circadian rhythms, eating behaviors, and the gastrointestinal microbiota and their potential impact on health. Nutr Rev. 2017;75(9):673-682.
  5. Bandin C, Scheer FA, Lugue AJ, et al. Meal timing affects glucose tolerance, substrate oxidation and circadian-related variables: a randomized, crossover trial. Int J Obes (Lond). 2015;39(5):828-833.
  6. Garaulet M, Gomez-Abellan P, Alburquerque-Bejar JJ, Lee YC, Ordovas JM, Scheer FA. Timing of food intake predicts weight loss effectiveness. Int J Obes (Lond). 2013;37(4):604-611.
  7. Jakubowicz D, Barnea M, Wainstein J, Froy O. High caloric intake at breakfast vs. dinner differentially influences weight loss of overweight and obese women. Obesity (Silver Spring). 2013;21(12):2504-2512.
  8. Goodson JM, Groppo D, Halem S, Carpino E. Is obesity an oral bacterial disease? J Dent Res. 2009;88(6):519-523.
  9. Damms-Machado A, Mitra S, Schollenberger AE, et al. Effects of surgical and dietary weight loss therapy for obesity on gut microbiota composition and nutrient absorption. Biomed Res Int. 2015;2015:806248.
  10. Takeshita T, Kageyama S, Furuta M, et al. Bacterial diversity in saliva and oral health-related conditions: the Hisayama Study. Sci Rep. 2016;6:22164.
  11. Collado MC, Engen PA, Bandin C, et al. Timing of food intake impacts daily rhythms of human salivary microbiota: a randomized, crossover study. FASEB J. 2018;32(4):2060-2072.
  12. Goodson JM, Hartman ML, Shi P, et al. The salivary microbiome is altered in the presence of a high salivary glucose concentration. PLoS One. 2017;12(3):e0170437.


Leave a Reply

Metagenics Institute is a trusted, peer-to-peer, evidence-based educational resource for nutrition and personalized medicine.
At Metagenics Institute, we translate credible research with scientific integrity into innovative and actionable clinical
decision-making. Metagenics Institute supports a diverse practitioner base to optimize patient outcomes by shifting existing paradigms in healthcare. Our mission is to transform healthcare by inspiring and educating practitioners, and their patients, about personalized lifestyle medicine.

Sponsored by
© 2023 Metagenics Institute. All Rights Reserved