khushi singh.in

Research · Ongoing · 2026–2027

From gut to germline: can microbes leave notes for the next generation?

Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany

Organism: Drosophila melanogaster

The question

Can lactate made by gut bacteria reach a mother’s eggs, become a chemical tag on the histone proteins that package DNA, and influence how the next generation’s genes first switch on?

What parents eat, and the microbes they live with, may influence their children’s biology. One possible route runs through metabolism: lactate, made by our own cells and by gut bacteria, can be attached to histones (histone lactylation) and may change which genes are used. In fruit flies, I ask whether metabolism shapes histone marks in the early embryo, at the moment its own genes switch on.

The basics: food for genes

In short

Cells do not just read DNA; they read chemical marks on the histones that DNA wraps around, and some of these marks are made from products of metabolism. In 2019, lactate was found to become one of them, histone lactylation. Strong evidence I study whether metabolism, including lactate made by the mother’s cells and her gut bacteria, shapes histone marks in the fly embryo during the maternal-to-zygotic transition, when its own genes first switch on. Hypothesis

It builds on three lines of published work: marks laid down in the egg guide the fly embryo’s first genes; gut microbes change how eggs are made and the timing of the hand-over in the offspring; and in mouse embryos lactate and a lactyl mark help the genome wake up. Strong evidence The same flies also let me ask how metabolism shapes behaviour, in my behavioural studies.

  1. Lactate is made

    by gut bacteria and by the mother’s own cells

  2. Into the egg?

    from the mother’s body

  3. Stage 5 embryo

    the maternal-to-zygotic transition

  4. Histone marks change?

    lactylation and acetylation as the embryo’s genes switch on

Hypothesis The chain I am exploring. Every arrow is an open question. No results are shown here.

The background, step by step. Open a block to read it here.

Why lactate?

A fuel, a signal and, since 2019, a histone mark

Lactate is made from pyruvate at the end of glycolysis and moves between cells as a fuel, the “lactate shuttle” (Brooks 2018). In 2019, researchers found 28 lactylation sites on core histones and showed that lactate made by glycolysis drives histone lactylation, so a product of sugar breakdown can directly mark chromatin (Zhang et al. 2019). Strong evidence

  • Fuel: cells pass lactate to their neighbours, which burn it in mitochondria (Brooks 2018).
  • Mark: lactate-derived lactylation on histones such as H3K18 (Zhang et al. 2019).
  • In embryos: in mouse and human embryos, lactate gathers in the nucleus as the major wave of genome activation begins (Li et al. 2024).
Papers mentioning “lactylation”, per year
02004006008001,0001,2001,400Papers per year20192020202120222023202420252026*5522791393791,0021,235

* 2026 is a partial year.

Source: PubMed via NCBI E-utilities, retrieved 2026-10-03.

Show the numbers
YearPapers
20195
20205
202122
202279
2023139
2024379
20251,002
2026*1,235

From sugar to lactate

The ten steps of glycolysis, and how lactate moves between cells

Glycolysis turns one glucose into two pyruvate, using 2 ATP and making 4, plus 2 NADH. Lactate dehydrogenase (LDH) turns pyruvate into lactate and regenerates the NAD⁺ that glycolysis needs to continue. Lactate crosses cell membranes on carrier proteins, in whichever direction the gradients favour, so lactate made in one cell can be used by another (Brooks 2018). In the receiving cell lactate becomes pyruvate again, feeding the TCA cycle and acetyl-CoA, and by routes still debated it contributes to the lactyl-CoA used for histone lactylation (Wellen et al. 2009; Zhang et al. 2019).

A cell that makes lactateA cell that takes lactate upspace between cellsGlut1glucoseinvestment: 2 ATP inpayoff, twice: 4 ATP + 2 NADH out · net 2 ATPHexokinase (Hex-A)ATP → ADPPhosphoglucose isomerase (Pgi)Phosphofructokinase (Pfk)ATP → ADPAldolase (Ald1)splits into two 3-carbon sugarsGAPDH (Gapdh1/2)NAD⁺ → NADH (×2 from here)Phosphoglycerate kinase (Pgk)ADP → ATPPhosphoglycerate mutase (Pglym78)Enolase (Eno)− H₂OPyruvate kinase (Pyk)ADP → ATPLactate dehydrogenase (Ldh)NADH → NAD⁺GlucoseGlucose-6-phosphateFructose-6-phosphateFructose-1,6-bisphosphateGlyceraldehyde-3-phosphate1,3-Bisphosphoglycerate3-Phosphoglycerate2-PhosphoglyceratePhosphoenolpyruvatePyruvateLactateDHAPTpiNAD⁺ recycled: glycolysis keeps goingcarriercarrierlactate+ H⁺carriers move lactate with a proton,down its gradient, in either directionLactateLDHNAD⁺ → NADHPyruvatemitochondrionPDHAcetyl-CoATCAcitrate(ATPCL)Acetyl-CoALactyl-CoAroute still beingworked outnucleuslahistonelactylationachistoneacetylationwritten by enzymes such as p300
From sugar to histone marks. Left: the ten steps of glycolysis, with fly gene names in brackets. Lactate dehydrogenase (LDH) turns pyruvate into lactate and gives back the NAD⁺ that GAPDH needs, so glycolysis can keep running. Middle: carrier proteins move lactate, together with a proton, between cells. Right: a cell that takes lactate up can burn it in mitochondria, use it to make acetyl-CoA for histone acetylation, or, by routes still being worked out, turn it into lactyl-CoA for histone lactylation. Schematic, drawn for this site from Berg et al. (textbook), Brooks 2018, Wellen et al. 2009 and Zhang et al. 2019.

How metabolism writes on histones

Acetyl, methyl and lactyl marks and their donors

Enzymes add acetyl groups from acetyl-CoA, methyl groups from SAM, and lactyl groups from lactyl-CoA; others remove methyl groups and need α-ketoglutarate from the TCA cycle. These enzymes work near the concentrations of their metabolites in the cell, so when the metabolites rise or fall, the marks can follow (Reid et al. 2017; Dai et al. 2020). Acetylation and H3K4me3 tend to mark active genes, H3K9me3 and H3K27me3 silent regions. Established Lactylation (for example H3K18la) is newer: its writers, donors and readers are still being defined, and its effect depends on context, activating in immune cells but sitting on silent meiotic chromatin in the fly oocyte (Zhang et al. 2019; Hayashi et al. 2025). Emerging

H3 · H4 · H2A · H2Btwo of eachnucleosome: DNA wrapped aroundeight histone proteinsK4me3K9me3K14acK18laK27acme3histone H3 tail(first 30 amino acids)K27: acetyl or methyl,never both at onceacK16histone H4 tailFood or pathwayDonor metaboliteMarkExamples · what they usually meanGlucose, fatty acidsAcetyl-CoAAcetylationH3K27ac, H4K16ac: loosens chromatin; marks active genesMethionineSAM (S-adenosylmethionine)MethylationH3K4me3 · H3K9me3, H3K27me3: active genes · silent regionsGlucose → lactateLactyl-CoALactylationH3K18la: active genes (immune cells); egg meiotic chromatin (fly)TCA cycleα-KetoglutarateDemethylationremoves methyl marks: needed by JmjC demethylases
Marks on histone tails, and where their chemistry comes from. Lysine (K) positions are those of histone H3 and H4. Enzymes add marks using donor metabolites, so the cell’s metabolism can change how much of each mark is made. Acetylation and methylation are well established; lactylation was discovered in 2019 and its roles are still being mapped. Schematic, drawn for this site from Reid et al. 2017, Dai et al. 2020, Zhang et al. 2019 and Hayashi et al. 2025.

The fly germline: testis and ovary

Lactate-fed germ cells, metabolism in the egg chamber

The germ line, the cells that become eggs and sperm, is where a parent’s metabolism could reach the next generation. In flies, both sexes show tight links between metabolism, support cells and germ cells.

The male germline: the testis

hub (niche)germline stem cellsdividing germ cells (2 → 16), eachcyst wrapped by two cyst cellssugar from the bloodspermatocyteslactateto germ cells
The testis feeds its germ cells lactate. Germ cells (green) develop inside a barrier of somatic cyst cells (magenta). Those cyst cells take up sugars from the blood, break them down to lactate and pass it on to the germ cells (orange arrows), which need it to survive (Sainz de la Maza et al. 2026). Concept redrawn for this site; anatomy after de Cuevas & Matunis 2011 and Fuller 1998. Not to scale.
  • Lactate feeds germ cells. Somatic cyst cells form a barrier around the germ cells, break down sugars from the blood and shuttle lactate to the germ cells, which need it to survive. If the support cells burn more sugar themselves, more germ cells die (Sainz de la Maza et al. 2026). Strong evidence
  • Like mammals. In mammals, Sertoli cells similarly supply lactate to developing sperm (Boussouar & Benahmed 2004). Established
  • The gut talks to the testis. The testis makes part of the male gut handle sugar differently, and gut-derived citrate supports sperm production (Hudry et al. 2019). Strong evidence
  • Sperm chromatin is repacked. During sperm maturation most histones are replaced by protamine-like proteins (Rathke et al. 2014), yet a father’s sugary diet still changes H3K9me3/H3K27me3-marked domains in his sperm and offspring (Öst et al. 2014). Emerging

The female germline: ovary and egg

  1. Follicle cells (somatic) need glycolysis to survive and divide; the germline stem cells and their early daughters do not, although cysts without it grow slowly. (Wessel & Drummond-Barbosa 2026) Strong evidence
  2. Nurse cells make the mother’s RNAs and proteins for the egg; without glycolysis their chromatin fails to spread out normally. (Wessel & Drummond-Barbosa 2026) Emerging
  3. Histone lactylation sits mainly on the oocyte’s tightly packed meiotic chromatin (the karyosome), a silent state, unlike its activating role in immune cells. (Hayashi et al. 2025) Emerging
  4. Late in oogenesis the oocyte’s mitochondria switch to a quiet, low-respiration state and the egg stores glycogen; reduced insulin signalling triggers this through GSK3. (Sieber et al. 2016) Strong evidence
  5. Marks laid down in the egg, such as H3K27me3 and H4K16ac, are passed to the embryo and help steer which genes switch on at the maternal-to-zygotic transition. (Zenk et al. 2017; Samata et al. 2020) Strong evidence
Metabolism and chromatin in the egg chamber. A stage 10 egg chamber: nurse cells (blue nuclei) at the front, the oocyte (green) at the back, follicle cells (magenta) around them. The numbers mark what published studies have found. Gut bacteria also shape how eggs are made (Elgart et al. 2016). Schematic drawn for this site.

Stage 5 and the maternal-to-zygotic transition

Where the question meets the embryo

Stage 5 (130–170 minutes after egg laying at 25 °C) is the cellular blastoderm, the heart of the maternal-to-zygotic transition (Tadros & Lipshitz 2009). Maternal H3K27me3 and H4K16ac help shape which genes switch on (Zenk et al. 2017; Samata et al. 2020). In mouse 2-cell embryos, blocking lactate production or uptake stalls the major wave of genome activation and removes H3K18la, which marks the promoters of most major-wave genes (Li et al. 2024). In Drosophila, lactylation has been mapped during oogenesis but not in the embryo at genome activation (Hayashi et al. 2025), and gut microbes change the timing of the transition in offspring (Elgart et al. 2016). A maternal or microbial metabolic input into stage 5 chromatin is plausible but untested. Hypothesis

See the stages, from egg chamber to stage 5 →

  • Mouse and human: lactate and H3K18la needed for the major wave of genome activation Emerging
  • Fly egg: lactylation on meiotic chromatin Emerging
  • Fly stage 5 embryo: unknown, the focus of this project Hypothesis

Environmental stress and histone marks

Heat, diet, oxygen and microbes

Stress and nutrition reach chromatin through signalling, such as a stress kinase releasing a chromatin protein (Seong et al. 2011), and through metabolism, such as more lactate or more acetyl-CoA (Wellen et al. 2009; Zhang et al. 2019). Some changes reach the germ line and the offspring: a father’s diet alters H3K9/K27me3-marked domains in sperm and embryos (Öst et al. 2014). Most of these are single studies, and how lasting such changes are in animals is still contested. Debated

  • Heat or salt stress

    Fruit fly embryos

    A stress kinase pulls the protein dATF-2 off heterochromatin, so tightly packed (HP1-bound) chromatin loosens. The loosened state was passed on for several generations before slowly returning to normal.

    Seong et al. 2011 Emerging

  • A father’s sugary diet

    Fruit flies

    Two days of extra sugar in fathers made their offspring prone to obesity. Silenced chromatin domains (marked by H3K9me3 and H3K27me3) opened up in sperm and in the embryos.

    Öst et al. 2014 Emerging

  • Low oxygen and infection

    Mouse and human cells

    Both push cells to make more lactate by glycolysis, and more lactate means more histone lactylation (such as H3K18la), which later switches on healing genes in immune cells.

    Zhang et al. 2019 Strong evidence

  • How much sugar is available

    Mammalian cells

    Histone acetylation follows glucose supply, because the enzyme ATP-citrate lyase turns glucose-derived citrate into the acetyl-CoA that acetylation uses.

    Wellen et al. 2009 Strong evidence

  • Losing the gut bacteria

    Fruit flies

    Germ-free mothers make fewer eggs, and in their offspring the maternal-to-zygotic transition happens earlier, a sign that microbes can reach the germ line.

    Elgart et al. 2016 Emerging

  • Blocking lactate in the early embryo

    Mouse and human embryos

    Lactate gathers in embryo nuclei at the major wave of genome activation. Blocking its production and uptake stops embryos at the 2-cell stage and removes H3K18la, a mark found on the promoters of most genes switched on at that wave.

    Li et al. 2024 Emerging

Sources

23 papers and books behind these blocks
  1. Zhang D, et al. 2019. Metabolic regulation of gene expression by histone lactylation. Nature 574:575–580. doi:10.1038/s41586-019-1678-1
  2. Brooks GA. 2018. The science and translation of lactate shuttle theory. Cell Metabolism 27:757–785. doi:10.1016/j.cmet.2018.03.008
  3. Berg JM, Tymoczko JL, Gatto GJ, Stryer L. 2019. Biochemistry, 9th edition. W. H. Freeman. (Glycolysis.)
  4. Tennessen JM, Barry WE, Cox J, Thummel CS. 2014. Methods for studying metabolism in Drosophila. Methods 68:105–115. doi:10.1016/j.ymeth.2014.02.034
  5. Wellen KE, et al. 2009. ATP-citrate lyase links cellular metabolism to histone acetylation. Science 324:1076–1080. doi:10.1126/science.1164097
  6. Sainz de la Maza D, et al. 2026. Somatic cells compartmentalise their carbohydrate metabolism to sustain germ cell survival. EMBO Journal 45:4910–4930. doi:10.1038/s44318-026-00815-y
  7. Reid MA, Dai Z, Locasale JW. 2017. The impact of cellular metabolism on chromatin dynamics and epigenetics. Nature Cell Biology 19:1298–1306. doi:10.1038/ncb3629
  8. Dai Z, Ramesh V, Locasale JW. 2020. The evolving metabolic landscape of chromatin biology and epigenetics. Nature Reviews Genetics 21:737–753. doi:10.1038/s41576-020-0270-8
  9. Hayashi Y, et al. 2025. Comprehensive observation of histone lysine lactylation during gametogenesis of Drosophila melanogaster. Developmental Dynamics 254:1230–1242. doi:10.1002/dvdy.70010
  10. de Cuevas M, Matunis EL. 2011. The stem cell niche: lessons from the Drosophila testis. Development 138:2861–2869. doi:10.1242/dev.056242
  11. Fuller MT. 1998. Genetic control of cell proliferation and differentiation in Drosophila spermatogenesis. Seminars in Cell & Developmental Biology 9:433–444. doi:10.1006/scdb.1998.0227
  12. Hudry B, et al. 2019. Sex differences in intestinal carbohydrate metabolism promote food intake and sperm maturation. Cell 178:901–918. doi:10.1016/j.cell.2019.07.029
  13. Rathke C, Baarends WM, Awe S, Renkawitz-Pohl R. 2014. Chromatin dynamics during spermiogenesis. Biochimica et Biophysica Acta 1839:155–168. doi:10.1016/j.bbagrm.2013.08.004
  14. Öst A, et al. 2014. Paternal diet defines offspring chromatin state and intergenerational obesity. Cell 159:1352–1364. doi:10.1016/j.cell.2014.11.005
  15. Boussouar F, Benahmed M. 2004. Lactate and energy metabolism in male germ cells. Trends in Endocrinology & Metabolism 15:345–350. doi:10.1016/j.tem.2004.07.003
  16. Wessel EM, Drummond-Barbosa D. 2026. Glycolysis is intrinsically required in the follicle stem cell lineage but not in female germline stem cells or their early progeny in Drosophila melanogaster. Genetics 232:iyag015. doi:10.1093/genetics/iyag015
  17. Sieber MH, Thomsen MB, Spradling AC. 2016. Electron transport chain remodeling by GSK3 during oogenesis connects nutrient state to reproduction. Cell 164:420–432. doi:10.1016/j.cell.2015.12.020
  18. Zenk F, et al. 2017. Germ line–inherited H3K27me3 restricts enhancer function during maternal-to-zygotic transition. Science 357:212–216. doi:10.1126/science.aam5339
  19. Samata M, et al. 2020. Intergenerationally maintained histone H4 lysine 16 acetylation is instructive for future gene activation. Cell 182:127–144. doi:10.1016/j.cell.2020.05.026
  20. Elgart M, et al. 2016. Impact of gut microbiota on the fly’s germ line. Nature Communications 7:11280. doi:10.1038/ncomms11280
  21. Tadros W, Lipshitz HD. 2009. The maternal-to-zygotic transition: a play in two acts. Development 136:3033–3042. doi:10.1242/dev.033183
  22. Li J, et al. 2024. Lactate regulates major zygotic genome activation by H3K18 lactylation in mammals. National Science Review 11:nwad295. doi:10.1093/nsr/nwad295
  23. Seong KH, Li D, Shimizu H, Nakamura R, Ishii S. 2011. Inheritance of stress-induced, ATF-2-dependent epigenetic change. Cell 145:1049–1061. doi:10.1016/j.cell.2011.05.029

How I work on it

I combine fruit-fly genetics with quantitative imaging of histone marks in early embryos, and with assays of fertility and behaviour.

Why it matters

If metabolism, or the microbes a mother lives with, can mark the embryo’s chromatin, it would be a concrete, testable route from the environment of parents to the biology of their children, a central idea behind the developmental origins of health and disease (DOHaD). Flies cannot tell us what happens in people, but they can show which mechanisms are worth looking for.

Open questions I find exciting

  • Bacteria make both L- and D-lactate. Which forms, if any, reach the germline?
  • Is lactate in the egg made by the mother’s own cells, by microbes, or both?
  • In the fly oocyte, lactylation sits on tightly packed meiotic chromatin. Is the mark activating or repressive in the early embryo?
  • Do fathers contribute too?

Methods used

  • Fruit-fly genetics
  • Immunostaining of early embryos
  • Confocal microscopy
  • Quantitative image analysis
  • Fertility and behaviour assays

What these methods are →

References

  1. Zhang D, et al. (2019) Metabolic regulation of gene expression by histone lactylation. Nature 574:575–580. doi:10.1038/s41586-019-1678-1
  2. Zenk F, et al. (2017) Germ line-inherited H3K27me3 restricts enhancer function during maternal-to-zygotic transition. Science 357:212–216. doi:10.1126/science.aam5339
  3. Samata M, et al. (2020) Intergenerationally maintained histone H4 lysine 16 acetylation is instructive for future gene activation. Cell 182:127–144. doi:10.1016/j.cell.2020.05.026
  4. Iatsenko I, Boquete JP, Lemaitre B (2018) Microbiota-derived lactate activates production of reactive oxygen species by the intestinal NADPH oxidase Nox and shortens Drosophila lifespan. Immunity 49:929–942. doi:10.1016/j.immuni.2018.09.017
  5. Elgart M, et al. (2016) Impact of gut microbiota on the fly’s germ line. Nature Communications 7:11280. doi:10.1038/ncomms11280
  6. Li J, et al. (2024) Lactate regulates major zygotic genome activation by H3K18 lactylation in mammals. National Science Review 11:nwad295. doi:10.1093/nsr/nwad295
  7. Hayashi Y, et al. (2025) Comprehensive observation of histone lysine lactylation during gametogenesis of Drosophila melanogaster. Developmental Dynamics 254:1230–1242. doi:10.1002/dvdy.70010
  8. Sainz de la Maza D, et al. (2026) Somatic cells compartmentalise their carbohydrate metabolism to sustain germ cell survival. EMBO Journal 45:4910–4930. doi:10.1038/s44318-026-00815-y