Diurnal oscillations in gut bacterial load and composition eclipse seasonal and lifetime dynamics in wild meerkats

AbstractCircadian rhythms in gut microbiota composition are crucial for metabolic function, yet the extent to which they govern microbial dynamics compared to seasonal and lifetime processes remains unknown. Here, we investigate gut bacterial dynamics in wild meerkats (Suricata suricatta) over a 20-year period to compare diurnal, seasonal, and lifetime processes in concert, applying ratios of absolute abundance. We found that diurnal oscillations in bacterial load and composition eclipsed seasonal and lifetime dynamics. Diurnal oscillations were characterised by a peak in Clostridium abundance at dawn, were associated with temperature-constrained foraging schedules, and did not decay with age. Some genera exhibited seasonal fluctuations, whilst others developed with age, although we found little support for microbial senescence in very old meerkats. Strong microbial circadian rhythms in this species may reflect the extreme daily temperature fluctuations typical of arid-zone climates. Our findings demonstrate that accounting for circadian rhythms is essential for future gut microbiome research.

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The effects of Levilactobacillus brevis on the physiological parameters and gut microbiota composition of rats subjected to desynchronosis

Microbial Cell Factories ◽

10.1186/s12934-021-01716-x ◽

2021 ◽

Vol 20 (1) ◽

Author(s):

Evgenii I. Olekhnovich ◽

Ekaterina G. Batotsyrenova ◽

Roman A. Yunes ◽

Vadim A. Kashuro ◽

Elena U. Poluektova ◽

...

Keyword(s):

Circadian Rhythms ◽

Gut Microbiota ◽

Relative Abundance ◽

Reduced Glutathione ◽

Physiological Parameters ◽

Male Rats ◽

Constant Light ◽

Constant Darkness ◽

Microbiota Composition ◽

Gut Microbiota Composition

Abstract Background All living organisms have developed during evolution complex time-keeping biological clocks that allowed them to stay attuned to their environments. Circadian rhythms cycle on a near 24 h clock. These encompass a variety of changes in the body ranging from blood hormone levels to metabolism, to the gut microbiota composition and others. The gut microbiota, in return, influences the host stress response and the physiological changes associated with it, which makes it an important determinant of health. Lactobacilli are traditionally consumed for their prophylactic and therapeutic benefits against various diseases, namely, the inflammatory bowel syndrome, and even emerged recently as promising psychobiotics. However, the potential role of lactobacilli in the normalization of circadian rhythms has not been addressed. Results Two-month-old male rats were randomly divided into three groups and housed under three different light/dark cycles for three months: natural light, constant light and constant darkness. The strain Levilactobacillus brevis 47f was administered to rats at a dose of 0.5 ml per rat for one month and The rats were observed for the following two months. As a result, we identified the biomarkers associated with intake of L. brevis 47f. Changing the light regime for three months depleted the reserves of the main buffer in the cell—reduced glutathione. Intake of L. brevis 47f for 30 days restored cellular reserves of reduced glutathione and promoted redox balance. Our results indicate that the levels of urinary catecholamines correlated with light/dark cycles and were influenced by intake of L. brevis 47f. The gut microbiota of rats was also influenced by these factors. L. brevis 47f intake was associated with an increase in the relative abundance of Faecalibacterium and Roseburia and a decrease in the relative abundance of Prevotella and Bacteroides. Conclusions The results of this study show that oral administration of L. brevis 47f, for one month, to rats housed under abnormal lightning conditions (constant light or constant darkness) normalized their physiological parameters and promoted the gut microbiome's balance.

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Current Applications of Absolute Bacterial Quantification in Microbiome Studies and Decision-Making Regarding Different Biological Questions

Microorganisms ◽

10.3390/microorganisms9091797 ◽

2021 ◽

Vol 9 (9) ◽

pp. 1797

Author(s):

Xiaofan Wang ◽

Samantha Howe ◽

Feilong Deng ◽

Jiangchao Zhao

Keyword(s):

Decision Making ◽

Relative Abundance ◽

Quantitative Methods ◽

High Throughput Sequencing ◽

Bacterial Load ◽

Data Interpretation ◽

Absolute Quantification ◽

Large Sample Size ◽

Absolute Abundance ◽

Host Interactions

High throughput sequencing has emerged as one of the most important techniques for characterizing microbial dynamics and revealing bacteria and host interactions. However, data interpretation using this technique is mainly based on relative abundance and ignores total bacteria load. In certain cases, absolute abundance is more important than compositional relative data, and interpretation of microbiota data based solely on relative abundance can be misleading. The available approaches for absolute quantification are highly diverse and challenging, especially for quantification in differing biological situations, such as distinguishing between live and dead cells, quantification of specific taxa, enumeration of low biomass samples, large sample size feasibility, and the detection of various other cellular features. In this review, we first illustrate the importance of integrating absolute abundance into microbiome data interpretation. Second, we briefly discuss the most widely used cell-based and molecular-based bacterial load quantification methods, including fluorescence spectroscopy, flow cytometry, 16S qPCR, 16S qRT-PCR, ddPCR, and reference spike-in. Last, we present a specific decision-making scheme for absolute quantification methods based on different biological questions and some of the latest quantitative methods and procedure modifications.

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Maternal milk microbiota and oligosaccharides contribute to the infant gut microbiota assembly

ISME Communications ◽

10.1038/s43705-021-00021-3 ◽

2021 ◽

Vol 1 (1) ◽

Author(s):

Martin Frederik Laursen ◽

Ceyda T. Pekmez ◽

Melanie Wange Larsson ◽

Mads Vendelbo Lind ◽

Chloe Yonemitsu ◽

...

Keyword(s):

Breast Milk ◽

Gut Microbiota ◽

Bacterial Load ◽

Fecal Microbiota ◽

Oral Bacteria ◽

Lactation Period ◽

Absolute Abundance ◽

Associated Bacteria ◽

Maternal Milk ◽

Changes Over Time

AbstractBreastfeeding protects against diseases, with potential mechanisms driving this being human milk oligosaccharides (HMOs) and the seeding of milk-associated bacteria in the infant gut. In a cohort of 34 mother–infant dyads we analyzed the microbiota and HMO profiles in breast milk samples and infant’s feces. The microbiota in foremilk and hindmilk samples of breast milk was compositionally similar, however hindmilk had higher bacterial load and absolute abundance of oral-associated bacteria, but a lower absolute abundance of skin-associated Staphylococcus spp. The microbial communities within both milk and infant’s feces changed significantly over the lactation period. On average 33% and 23% of the bacterial taxa detected in infant’s feces were shared with the corresponding mother’s milk at 5 and 9 months of age, respectively, with Streptococcus, Veillonella and Bifidobacterium spp. among the most frequently shared. The predominant HMOs in feces associated with the infant’s fecal microbiota, and the dominating infant species B. longum ssp. infantis and B. bifidum correlated inversely with HMOs. Our results show that breast milk microbiota changes over time and within a feeding session, likely due to transfer of infant oral bacteria during breastfeeding and suggest that milk-associated bacteria and HMOs direct the assembly of the infant gut microbiota.

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Microbial dynamics and physico-chemical properties of artisanal refinery polluted environment in Niger Delta

GSC Biological and Pharmaceutical Sciences ◽

10.30574/gscbps.2021.15.3.0142 ◽

2021 ◽

Vol 15 (3) ◽

pp. 001-015

Author(s):

Mobene Eneriene Luke ◽

Lucky Obukowho Odokuma ◽

Chimezie Jason Ogugbue

Keyword(s):

Niger Delta ◽

Bacterial Species ◽

Bacterial Load ◽

Chemical Properties ◽

Pollution Index ◽

Environmental Water ◽

Microbial Dynamics ◽

Soil Matrix ◽

Niger Delta Region ◽

Physico Chemical

Artisanal refining of crude oil is a common practice in the Niger Delta region of Nigeria and this has continuously posed serious environmental and health risks. This was designed to investigate the microbial dynamics and physico-chemical properties of environmental (water, sediment and soil) matrix of impacted by artisanal refining activities. Three sampling locations (Bolo, River’s state; Ekpemu, Delta state; and Twon-Brass, Bayelsa state) were studied. Finding revealed that the total heterotrophic bacterial (THB) load of the recipient water from Twon-Brass had the least count of 2.0 ±0.2 x 104cfu/ml, followed by Ekpemu (2.1 ±0.3 x 103cfu/ml), then Bolo (2.35±0.6 x 104cfu/ml). In the contrary, recipient water body in Ekpemu had the least HUB load (1.8 ±0.1 x 103cfu/ml) followed by Bolo (2.0 ±0.3 x 104cfu/ml), and Twon-Brass (2.0 ±0.8 x 104cfu/ml). The bacterial load of the un-impacted aquatic matrix revealed a higher heterotrophic bacterial load (5.8+ 0.30 x 105cfu/ml) and low HUB load (0.2+ 0.21 x 103cfu/ml). In the sediment, Bodo had the least THB load of 2.1 ±0.2 x 105cfu/g, followed by Twon-Brass (2.3 ±0.6 x 105cfu/g), and Ekpemu (2.9 ±0.3 x 105cfu/g).Bolo and Twon-Brass soil were also highly impacted with hydrocarbons with a pollution index close to 1 (HUB/THB ratio = 0.9) while Ekpemu had a pollution index of 0.7. Bacterial species associated with the samples were Bacillus subtilis, Pseudomonas putida, and Pseudomonas aeruginosa were predominant in all the sample locations. Similarly, the artisanal refining activities also altered the physico-chemical properties of the various environmental matrix studied. Based on the finding of this study, it can be predicted that bioremediation various environmental matrix by natural attenuation is ongoing as most of the organisms isolated are hydrocarbon degraders. However, it is recommended that artisanal refining activities should be discouraged.

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Combining integrated systems-biology approaches with intervention-based experimental design provides a higher-resolution path forward for microbiome research

Behavioral and Brain Sciences ◽

10.1017/s0140525x18002911 ◽

2019 ◽

Vol 42 ◽

Author(s):

J. Alfredo Blakeley-Ruiz ◽

Carlee S. McClintock ◽

Ralph Lydic ◽

Helen A. Baghdoyan ◽

James J. Choo ◽

...

Keyword(s):

Systems Biology ◽

High Resolution ◽

Experimental Design ◽

Integrated Systems ◽

Microbiome Research ◽

Constructive Criticism

Abstract The Hooks et al. review of microbiota-gut-brain (MGB) literature provides a constructive criticism of the general approaches encompassing MGB research. This commentary extends their review by: (a) highlighting capabilities of advanced systems-biology “-omics” techniques for microbiome research and (b) recommending that combining these high-resolution techniques with intervention-based experimental design may be the path forward for future MGB research.

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Inter-individual variation shapes the human microbiome

Behavioral and Brain Sciences ◽

10.1017/s0140525x1800287x ◽

2019 ◽

Vol 42 ◽

Author(s):

Emily F. Wissel ◽

Leigh K. Smith

Keyword(s):

Individual Differences ◽

Individual Variation ◽

Human Microbiome ◽

Individual Variability ◽

Microbiota Composition ◽

Target Article ◽

Microbiome Research

Abstract The target article suggests inter-individual variability is a weakness of microbiota-gut-brain (MGB) research, but we discuss why it is actually a strength. We comment on how accounting for individual differences can help researchers systematically understand the observed variance in microbiota composition, interpret null findings, and potentially improve the efficacy of therapeutic treatments in future clinical microbiome research.

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The Biological Clock and Sleep in the Elderly

Zeitschrift für Gerontopsychologie & -psychiatrie ◽

10.1024/1011-6877.19.1.45 ◽

2006 ◽

Vol 19 (1) ◽

pp. 45-51 ◽

Cited By ~ 1

Author(s):

Myriam Juda ◽

Mirjam Münch ◽

Anna Wirz-Justice ◽

Martha Merrow ◽

Till Roenneberg

Keyword(s):

Circadian Rhythms ◽

Biological Clock ◽

The Elderly ◽

Early Morning ◽

Behavioral Changes ◽

Older Age ◽

Age Related ◽

Theoretical Considerations ◽

Sleep Difficulties ◽

Circadian Biology

Abstract: Among many other changes, older age is characterized by advanced sleep-wake cycles, changes in the amplitude of various circadian rhythms, as well as reduced entrainment to zeitgebers. These features reveal themselves through early morning awakenings, sleep difficulties at night, and a re-emergence of daytime napping. This review summarizes the observations concerning the biological clock and sleep in the elderly and discusses the documented and theoretical considerations behind these age-related behavioral changes, especially with respect to circadian biology.

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