Every human has got their own bacterial flora on their skin, in their gastrointestinal tract, genitourinary system and in the oral cavity, which is called the microbiome . The human microbiome is shaped by many different factors – newborn babies’ microbiomes depend on the labor type and way of feeding – natural breast milk or infant formula. Later, the micro biome is related to diet, age, sex, medications taken and diseases. Although microbiome formation varies, in adults, it is relatively stable. The microbiome is characteristic to a living host, but after death, there are specific changes of microbial phyla, genera and families. The microbiome of deceased humans is called the thanatomicrobiome (in Greek mythology Thanatos was the personification of death) [52, 98]. To estimate the PMI (post-mortem interval), a forensic medical examiner uses such indicators as: pallor mortis, algor mortis, rigor mortis, livores mortis, decomposition stages and insect activity – forensic entomology. It is proved that the changes in the thanatomicrobiome are characteristic and repeatable enough to become an additional PMI indicator . Research showed that the sequences of microbial phyla changes are nearly the same among mammals, and thus allow the expansion of the research area to animal models [20, 86].
Microbial communities change not only on cadavers. Burial places and the soil beneath cadavers during decomposition process also undergo microbial phyla changes [31, 88]. Also, like the changes in the thanatomicrobiome, bacteria shifts in soil are characteristic during particular decomposition phases. Different authors distinguish various number of decomposition stages – usually three to five decomposition stages appear in studies: fresh, bloat, active decay, advanced decay and the dry remains stage . For each stage, there is a specified bacterial phylapredominance, and increasing or decreasing bacteria abundance over time .
Living host microbiome and mycobiome
The skin microbiome consists of four main phyla: Actinobacteria, Bacteroidetes, Firmicutes and Proteobacteria. The most abundant genera are Staphylococcus spp. (mostly S. epidermidis), Corynebacterium, Propionibacterium, Brevibacterium and Micrococcus [42, 67].
In the oral cavity there is tremendous diversity of bacteria , predominantly Streptococcus, Veillonella, Fusobacterium, Neisseria, Haemophilus, Propionibacterium, Eikenella, Peptostreptococcus and Eubacteria . Nasal bacteria are Actinobacteria (Propionibacterium and Corynebacterium) and Firmicutes (Staphylococcus spp.) [33, 42].
The bronchi and lungs are colonized mostly with four phyla: Bacteroidetes, Firmicutes, Proteobacteria and Actinobacteria , [Table I]. The most common bacterial taxon in the esophagus is Streptococcus. Additionally, Haemophilus, Prevotella, Neisseria,and Veillonella may be present . The stomach is inhabited by Proteobacteria (Helicobacter pylori) and Firmicutes. In the intestines, two phyla dominate: Bacteroidetes and Firmicutes, most of intestinal bacteria are anaerobic: Bacteroides, Bifidobacterium, Fusobacterium, Eubacterium and Ruminococcus . However, in the intestines, aerobic and obligately anaerobic bacteria are present as well, for instance Enterobacter spp., Escherichia coli, Staphylococcus spp., Klebsiella spp. and Proteus spp. . In the vagina, the most abundant are Lactobacillus (L. crispatus, L. gasseri, L. iners oraz L. jensenii) .
Human microbiome in regard to body areas
Human mycobiome in regard to body areas
Microbiomes differ between individuals, and are related to diet, age, sex, weight, health status, antibiotic administration or even with cosmetic use . However, during across a one-year observation period, the intestinal microbiome in each host is relatively stable and varies to a small extent .
Fungal diversity in the human gut is much lower than bacterial diversity . The most abundant fungal genusin human stool is Candida, followed by Malassezia and Saccharomyces . Ascomycota is the most abundant phylum among fungi, not only in the stool but also in the vagina, oral cavity and skin . In the digestive tract, other sources [30, 82] additionally mention the Cladosporium and Cryptococcus genera, Eurotiales order and Botrysphaeriales asapopularfamily.
On the skin, the most abundant are Malassezia restrica and M. furfur, but M. globosa, M. sympodialis and M. pachydermatis are also frequently present . Candida may be component of the skin mycobiome but rarely colonize human skin – usually in diabetic patients or during infections . In the oral cavity, Candida, Saccharomyces, Penicillium, Scopularis, Geotrichum and Aspergillus are present [25, 26]. The bronchial and lung mycobiome is partially determined by oral and nasal fungi which spread through continuity. Therefore, in lower respiratory tract, the most abundant are: Cladosporium, Aspergillus, Candida, Malassezia and Saccharomyces. In the genitourinary system, the most common are: Saccharomyces, Candida, Aspergillus, Cladosporium and Alternaria.
During PMI estimation, it is important to know the medical history of the deceased person, because the microbiome in persons suffering from diseases is significantly different than a healthy human microbiome [8, 93].
Chronic alcohol abuse and cirrhosis cause a decrease of Clostridium presence and increase of Proteobacteria (Enterobacter)and Bacteroides spp. .
Diabetes mellitus patients showed a higher abundance of Bacteroidetes and lower percentage of Firmicutes in the intestinal microbiota . Necrotizing enterocolitis is correlated with high abundance of Proteobacteria .
Alzheimer’s disease corresponds to an abundance of Bacteroides fragilis and Escherichia coli and their neurotoxin, and the presence of bacterial lipopolysaccharide (LPS) in the brain in the hippocampal area . Allergies, cardiovascular diseases, cancer, psychiatric diseases and metabolic syndrome also affect the host microbiome .
Although there are no studies considering mistakes in PMI estimation caused by cadavers illnesses, individual abnormalities of quantity or phyla abundance can be compared with characteristic differences in particular disease. If the medical history of the cadaver is known, time since death can be confirmed more precisely,with bacterialnumberorpresencedeviation clarified by illness.
Thanatomicrobiome – human cadaver studies
A basic difficulty during cadaver studies is the cessation of natural barrier protection. After death, intestinal bacteria can move to the blood and tissues. Additionally other types of bacteriaalso begin to spread around the entire corpse. This is caused by tissue congestion, vessel enlargement and the unsealing of cell junctions. As a result, organs considered to be sterile can become settled by bacteria, and tissues where there is a specific microbiota can be contaminated by bacteria from other areas. For this reason, the longer the time since death, the lower the accuracy of the research.
Damann et al.  analyzed ribs of 12 human cadavers and divided decomposition into 3 phases – partially skeletonized, skeletonized and dry remains. It was proved that in two of the prime phases, the thanatomicrobiome was similar to a living human gut microbiome, while the dry remains phase was characterized by a thanatomicrobiome more similar to soil bacterial communities, but was not identical . The partially skeletonized and skeletonized stages had a high abundance of Firmicutes and Proteobacteria. During decomposition, Firmicutes decreased while Proteobacteria and Actinobacteria started increasing. In contrast to soil samples, cadaver thanatomicrobiomes in the last phasehadhigherlevelsof Actinobacteria, Bacteroidetes, Proteobacteria and Firmicutes and a smaller quantity of Acidobacteria.
DeBruyn et al.  divided decomposition into 2 phases, and showed that at the beginning, Bacteroidetes and Firmicutes predominated. In the late phase of decomposition, Firmicutes was still in abundance, while Bacteroidetes decreased and Ignatzschineria increased.
Mouth thanatomicrobiomes also vary in time – to start with, the main phyla were Firmicutes and Actinobacteria, while during bloat stage there was an increased number of Tenericutes, and growth of Ignatzschineria was also remarkable. Dry remains were characterized by a increase of Firmicutes with an abundance of Clostridiales and Bacillaceae .
Although an increasing number of studies widen the knowledge about thanatomicrobiome changes, it is worth noticing that scientists discover some differences related to illnesses or sex. For instance, Bell et al.  proved differences between the thanatomicrobiomes in male and female heart samples , taken from 10 cadavers and analyzed 6–58 h since death [Table III]. In male hearts, most abundant phyla was Firmicutes, while in females Proteobacteria predominated, Bacteroidetes was in similar quantity in both sexes. Bacilli and Streptococcaceae were detected almost solely in males. Lactobacillales, Rhizobiales were found only in males, while Pseudomonadales and Gammaproteobacteria were more abundant in female hearts samples. Clostridium sp. was present in both sexes in a similar percentage. Clostridium was present in almost all cadaver samples . There is rapid overgrowth after death, because Clostridium have the shortest doubling time. Bacteroides and Lactobacillus spp. decreased as far as decomposition progressed .
Most abundant phyla in human cadaver according to sex
Heart thanatomicrobiome differences in relation to sex
Fungi presence – thanatomycobiome
Although most thanatomicrobiome studies focus on bacteria, studies about fungal presence can be the equally as important in PMI estimation in both humans and animals . Human cadaver research is less frequent due to legal reasons and smaller number of donors, therefore animal research allows to extend more general knowledge on the subject. However, animal PMI estimation is also used independently in forensic veterinary medicine .
Research based on human studies showed fungi presence during three stages of decomposition (bloated, putrefaction and skeletonization) . Samples were taken from the cadaver’s mouth, skin, rectum, vagina, lungs and grave soil or coffin fragments. In the bloated stage, Aspergillus flavus was dominating, followed by Aspergillus niger and Penicillium rugulosum in all sampling locations. In the purification stage, Candida albicans dominated in most samples, except hair, in which the fungal pattern was the same as in bloated stage. The skeletonized stage was dominated by Penicillium, with presence of Aspergillus flavus and Aspergillus niger [Table IV].
Predominant phyla in 3 decomposition stages in particular corpse parts in order to frequency of appearance
Tranchida et al.  describes human cadavers in an advanced decomposition state. In soil samples beneath the remains, Talaromyces udagawae (Aspergillaceae), registered as human pathogen, was detected, while in control soil samples, there was no signs of T. udagawae. In soil samples from under the cadaver, Dichotomomyces cejpii and Talaromyces trachyspermus were also found. Other fungi – Mortierella, Mucor hiemalis, Aspergillus and Penicillium frequentas were detected in control soil samples taken 15 meters from the cadaver.
Xiaoliang Fu et al.  presented differences between fungal succession during decomposition inside and outside, using pigs carcasses. During the decomposition of 3 pigs indoors, Candida xylopsoci, Ascomycota spp. and Thermoascus aurantiacus dominated. The outdoor carcasses decomposed faster and the dominating fungi was Yarrowia lipolytica. In soil samples from beneath the carcasses, Yarrowia lipolytica and Candida catenulate dominated. During the initial decomposition stage, fungal succession on carcasses were similar but as decay proceeded, indoor and outdoor fungal succession startedtovary.
Thanatomicrobiome of frozen cadavers
A distinct issue is the thanatomicrobiome after long-term freezing. Hyde et al.  described 2 donated cadavers, the first frozen for 89 days, and the second for 143 days. In both cadavers, most popular phyla in the mouth was Firmicutes, followed by Actinobacteria on the first cadaver and Proteobacteria on the second one. As decomposition progressed, Actinobacteria decreased and Proteobacteria increased on the first cadaver. A second case, also presented by Hyde , described 2 cadavers, one frozen for 22 days and the second for 14 days. Firmicutes and Actinobacteria increased in the later phases of decomposition. Firmicutes and Bacteroides predominated in fecal samples before purge, while later stages of decomposition were dominated by Proteobacteria. There were differences between the thanatomicrobiome genus in the two cadavers in Hyde’s second research – the first cadaver was dominated by Ignatzschineria, Acinetobacter and Pseudomonas, while in the second cadaver, Clostridium, Acinetobacter and Ignatzschineria predominated. A third piece of research by Pechal et al.  was performed on 2 cadavers of children, aged 9 and 13, murdered and frozen by mother. In contrast to previous research, in this one, there were observed differences between bacterial diversity during the thawing process. While thawing, Actinobacteria, Fusobacteria and Gammaproteobacteria increased, and Firmicutes decreased. In reference to families – Corynebacteriaceae, Fusobacteriaceae, Pasteurellaceae, Pseudomonaceae and Tissierllaceae significantly increased, in contrast to Prevotellaceae and Staphylococcaceae which decreased.
Soil microbial community changes
Soil microbial communities are quite different in comparison to the human microbiome. This knowledge is crucial, because there is the possibility to prove the former presence of a buried or decomposing cadaver based on microbial changes in soil . A second option is estimating PMI by defining microbial communities on remains which are different in decomposition stages and are more similar to soil communities in late stages. Comparison of microbiome changes in the soil requires the appropriate collection of samples to differentiate soil related to thanatomicrobiome changes and a comparative soil sample, which is pure soil without contact with a cadaver and its thanatomicrobiome .
Proper sample collection includes taking soil samples right beneath the cadaver (0–5 cm) [17, 31, 84, 90] and control samples. A crucial assumption is receiving soil samples without contact with cadaver – most frequent distances, considered to be adequate, used in soil thanatomicrobiome studies are 1 m, 5 m and 15 m from the body [84, 90, 91].
Garriga et al.  proved that different bacterial phyla appear in particular decomposition stages, at first, Proteobacteria, Acidobacteria and Bacteroidetes predominate, while in later phases Firmicutes, Actinobacteria and Proteobacteria are more abundant,and finally Firmicutes and Proteobacteria are the most common [2, 30].
Finley et al.  described a one-year observation of soil microbiota beneath cadavers. Cadavers were divided into two groups – one was cadavers on the surface and the second group was buried bodies. In both groups, the predominant phylum was Proteobacteria, but in group of buried cadavers, the quantity of these bacteria was lower. Acidobacteria in the buried group was more abundant than in the surface group and in control samples. After 9 months, Firmicutes in the surface group was predominant phylum, in contrastto buriedgroupandcontrols,wheretheamountof Firmicutes was low. Acidobacteria and Verrucomicrobia were more abundant in the buried group.
Singh et al.  proved that the soil microbiome beneath cadavers is significantly different than the soil microbiome 1 m and 5 m from the cadaver. Right below the cadaver, the relative abundance of Firmicutes and Bacteroidetes was greater, but the amounts of Verrucomicrobia, Acidobacteria, Chloroflexi and Gemmatimonadetes were smaller. All of the cadavers were placed on a field, and the research included 732 days of sampling.
Cobaugh et al.  in research on four cadavers compared gut bacteria communities and soil microbiota beneath cadavers. The cadavers’ most abundant phyla were Bacteroidetes and Firmicutes, while in soil samples, the most common were Proteobacteria, Actinobacteria and Firmicutes. Actinobacteria and Firmicutes increased while decomposition progressed, in contrast to Acidobacteria and Verrucomicrobia which decreased.
There is also research on swine buried models , and in the soil samples, Proteobacteria was most abundant phylum, while the second most abundant phylum was Bacteroidetes, with Firmicutes increasing in later phases of decomposition. Control soil samples showed a predominance of Acidobacteria. Soil beneath the carcassescontainedareduced quantityof Acidobacteria but this phenomenon fluctuated in time and when pH raised, Acidobacteria abundance increased.
Rabbit decomposition research  demonstrated a predominant abundance of Proteobacteria,witha presence of Bacteroidetes and Actinobacteria. An interesting fact is that Actinobacteria was in higher abundance during early stages of decomposition, and in the group of rabbits with fur, the abundance of this phylum was definitely higher than in the bald rabbit group. In later stages of decomposition, the percentage of Actinobacteria in soil samples was nearly equal in both groups.
Season-related microbial changes
Research on rat carcasses considered different decom position patterns and microbiota in relation to different seasons. In the spring, swabs taken from the small intestine of carcasses showed that the predominant phylum was Proteobacteria, followed by Firmicutes. In the summer, the predominant phylum was Firmicutes. It is noticed that Enterococcus faecalis had different growth patterns in the spring and summer, but ultimately in both seasons, the abundance in carcasses was similar .
Benbow et al.  in research on swine carcasses in a river proved that there are some differences in decomposition during different seasons. The generally predominant phylum was Proteobacteria followed by Firmicutes and Bacteroidetes. In the summer, the decrease of Proteobacteria was slower than in the winter. In the winter, while decomposition progressed, Firmicutes abundance was, in general, higher than in the summer. In contrast to Firmicutes, Bacteroidetes was more abundant in the summer during all decomposition stages.
Another research on swine carcasses in water inthe autumn and winter  showed that there are some bacteria which are season-specific. Carnobacterium, Marinomonas, Aeromonas and Bacteroidales Genus 2 and 8 were present in autumn exclusively. Polaribacter and Bacteroidales Genus 4 were distinctive for winter.
Thanatomicrobiome and entomology correlation
After death, not only bacteria exist and graze on cadavers. Within minutes, chemical signals attract the first necrophagous flies . Calliphora vomitoria and Lucilia sericata are the most numerous insects in Europe detected on cavers, attracted by decomposition odor . Odors are chemical signals, which appear while bacteria start producing postmortem compounds. Bacteria are capable of producing or decomposing substances like indole, ammonia, putrescine, and benzoic acid during cadaver decomposition . Different substances attract various necrophagous flies, but ammonia is considered to be the interkingdom signal that controls the activity of bacteria and blow flies . Also, thereis a correlation between insect and bacteria genus occurrence on cadavers [Table V] . Relations between bacteria and blowflies work both ways – some bacteria, like Proteus mirabilis, occur on cadavers, transferred bythesalivaryglandsof blowfly Lucilia sericata. The burying beetle transfers its own gut microbiome onto the cadaver – Morganella, Proteus, Providencia, Vagococcus, Xanthomonadaceae and Tissirella . On the other hand, insects, like burying beetles, struggle to obtain the carbohydrates, lipids and proteins present in the cadaver. For this purpose, insects participate in spreading oral secretions that have antibacterial activity, helping to restrain bacterial proliferation .
Correlation between bacteria and insects ocurrence on cadaver
Studies in general focus on the presence of insects on cadavers or on the thanatomicrobiome, and there is only a few examples of research on how both bacteria and insect presence are related , . It is clear that presence of some insects entails the appearance of some bacteria phyla and vice versa , but future studies may be able to clarify the correlation in later phases of decomposition and enable a precise definition of relations between the development of thanatomicrobiome phyla and insects in particulars decomposition stages.
Over the years, knowledge about microbiome changes decisively increased. A constantly rising number of scientific studies and research leads to the possibility of PMI estimation using the thanatomicrobiome. Nowadays, we can distinguish three to five decomposition stages basing on cadaver microbiomes and bacterial community shifts during decay. Moreover, distinctive microbiome changes in the soil beneath the remains, either on the surface or soil beside a buried cadaver, can equally precisely determine the time since death. Distinctive differences occur in thanatomicrobiome changesinwaterorduringthethawingprocesstoo. In addition, the microbiome on the cadaver is dependent on the season. Some bacteria can be transferred onto the cadaver by necrophagous insects. Furthermore, the microbiome is not the only indicator we can use in PMI estimations, as fungal changes after death (thanatomycobiome) are also characteristic and specific to different decomposition stages and body parts.
Some research focuses on differences between human decomposition and animal models. The final conclusion is that there is a sufficient similarity in different mammal decomposition stages, and process to expand animal model’s records to believable conclusions for the human cadaver decomposition model.
Adlam R.E., Simmons T.: The effect of repeated physical disturbance on soft tissue decomposition – are taphonomic studies an accurate reflection of decomposition? J. Forensic Sci. 52, 1007–1014 (2007)AdlamR.E.SimmonsT.The effect of repeated physical disturbance on soft tissue decomposition – are taphonomic studies an accurate reflection of decomposition?5210071014200710.1111/j.1556-4029.2007.00510.x17645488Search in Google Scholar
Adserias-Garriga J., Hernandez M., Quijada N.M., Lazaro D.R., Steadman D., Garcia-Gil J.: Daily thanatomicrobiome changes in soil as an approach of postmortem interval estimation: an ecological perspective. Forensic Sci. Int. 278, 388–395 (2017)Adserias-GarrigaJ.HernandezM.QuijadaN.M.LazaroD.R.SteadmanD.Garcia-GilJ.Daily thanatomicrobiome changes in soil as an approach of postmortem interval estimation: an ecological perspective.278388395201710.1016/j.forsciint.2017.07.01728818754Search in Google Scholar
Adserias-Garriga J., Hernandez M., Quijada N.M., Lazaro D.R., Steadman D., Garcia-Gil J.: Dynamics of the oral microbiota as a tool to estimate time since death. Mol. Oral Microbial. 32, 511–516 (2017)Adserias-GarrigaJ.HernandezM.QuijadaN.M.LazaroD.R.SteadmanD.Garcia-GilJ.Dynamics of the oral microbiota as a tool to estimate time since death.32511516201710.1111/omi.1219128654195Search in Google Scholar
Barton P.S., Reboldi A., Dawson B.M., Ueland M., Strong C., Wallman J.F.: Soil chemical markers distinguishing human and pig decomposition islands: a preliminary study. Forensic Sci. Med. Pat. 16, 605–612 (2020)BartonP.S.ReboldiA.DawsonB.M.UelandM.StrongC.WallmanJ.F.Soil chemical markers distinguishing human and pig decomposition islands: a preliminary study.16605612202010.1007/s12024-020-00297-232876891Search in Google Scholar
Bell C.R., Wilkinson J.E., Robertson B.K., Javan G.T.: Sex-related differences in the thanatomicrobiome in postmortem heart samples using bacterial gene regions v1–2 and v4. Lett. Appl. Microbiol. 67, 144–153 (2018)BellC.R.WilkinsonJ.E.RobertsonB.K.JavanG.T.Sex-related differences in the thanatomicrobiome in postmortem heart samples using bacterial gene regions v1–2 and v4.67144153201810.1111/lam.1300529747223Search in Google Scholar
Benbow M.E., Pechal J.L., Lang J.M., Erb E., Wallace J.R.: The potential of high-throughput metagenomic sequencing of aquatic bacterial communities to estimate the postmortem submersion interval. J. Forensic Sci. 60, 1500–1510 (2015)BenbowM.E.PechalJ.L.LangJ.M.ErbE.WallaceJ.R.The potential of high-throughput metagenomic sequencing of aquatic bacterial communities to estimate the postmortem submersion interval.6015001510201510.1111/1556-4029.1285926294275Search in Google Scholar
Benninger L., Carter D., Forbes S.: The biochemical alterations of soil beneath a decomposing carcass. Forensic Sci. Int. 180, 70–75 (2008)BenningerL.CarterD.ForbesS.The biochemical alterations of soil beneath a decomposing carcass.1807075200810.1016/j.forsciint.2008.07.00118752909Search in Google Scholar
Blum H.E.: The human microbiome. Adv. Med. Sci. 62, 414–420 (2017)BlumH.E.The human microbiome.62414420201710.1016/j.advms.2017.04.00528711782Search in Google Scholar
Burcham Z.M., Cowick C.A., Baugher C.N., Pechal J.L., Schmidt C.J., Rosch J.W., Benbow M.E., Jordan H.R.: Total RNA analysis of bacterial community structural and functional shifts throughout vertebrate decomposition. J. Forensic Sci. 64, 1707–1719 (2019)BurchamZ.M.CowickC.A.BaugherC.N.PechalJ.L.SchmidtC.J.RoschJ.W.BenbowM.E.JordanH.R.Total RNA analysis of bacterial community structural and functional shifts throughout vertebrate decomposition.6417071719201910.1111/1556-4029.1408331170333Search in Google Scholar
Burcham Z.M., Hood J.A., Pechal J.L., Krausz K.L., Bose J.L., Schmidt C.J., Benbow M.E., Jordan H.R.: Fluorescently labeled bacteria provide insight on post-mortem microbial transmigration. Forensic Sci. Int. 264, 63–69 (2016)BurchamZ.M.HoodJ.A.PechalJ.L.KrauszK.L.BoseJ.L.SchmidtC.J.BenbowM.E.JordanH.R.Fluorescently labeled bacteria provide insight on post-mortem microbial transmigration.2646369201610.1016/j.forsciint.2016.03.01927032615Search in Google Scholar
Can I., Javan G.T., Pozhitkov A.E., Noble P.A.: Distinctive thanatomicrobiome signatures found in the blood and internal organs of humans. J. Microbiol. Meth. 106, 1–7 (2014)CanI.JavanG.T.PozhitkovA.E.NobleP.A.Distinctive thanatomicrobiome signatures found in the blood and internal organs of humans.10617201410.1016/j.mimet.2014.07.02625091187Search in Google Scholar
Carter D.O., Metcalf J.L., Bibat A., Knight R.: Seasonal variation of postmortem microbial communities. Forensic Sci. Med. Pat. 11, 202–207 (2015)CarterD.O.MetcalfJ.L.BibatA.KnightR.Seasonal variation of postmortem microbial communities.11202207201510.1007/s12024-015-9667-725737335Search in Google Scholar
Carter D.O., Tibbett M.: Taphonomic mycota: fungi with forensic potential. J. Forensic Sci. 48, 168–171 (2003)CarterD.O.TibbettM.Taphonomic mycota: fungi with forensic potential.48168171200310.1520/JFS2002169Search in Google Scholar
Cernosek T., Eckert K.E., Carter D.O., Perrault K.A.: Volatile organic compound profiling from postmortem microbes using gas chromatography – mass spectrometry. J. Forensic Sci. 65, 134–143 (2019)CernosekT.EckertK.E.CarterD.O.PerraultK.A.Volatile organic compound profiling from postmortem microbes using gas chromatography – mass spectrometry.65134143201910.1111/1556-4029.1417331479524Search in Google Scholar
Chun L.P., Miguel M.J., Junkins E.N., Forbes S.L., Carter D.O.: An initial investigation into the ecology of culturable aerobic postmortem bacteria. Sci. Justice, 55, 394–401 (2015)ChunL.P.MiguelM.J.JunkinsE.N.ForbesS.L.CarterD.O.An initial investigation into the ecology of culturable aerobic postmortem bacteria.55394401201510.1016/j.scijus.2015.07.00326654073Search in Google Scholar
Clement C., Hill J.M., Dua P., Culicchia F., Lukiw W.J.: Analysis of RNA from Alzheimer’s disease post-mortem brain tissues. Mol. Neurobiol. 53, 1322–1328 (2016)ClementC.HillJ.M.DuaP.CulicchiaF.LukiwW.J.Analysis of RNA from Alzheimer’s disease post-mortem brain tissues.5313221328201610.1007/s12035-015-9105-6545016425631714Search in Google Scholar
Cobaugh K.L., Schaeffer S.M., DeBruyn J.M.: Functional and structural succession of soil microbial communities below decomposing human cadavers. Plos One, 10, e0130201 (2015)CobaughK.L.SchaefferS.M.DeBruynJ.M.Functional and structural succession of soil microbial communities below decomposing human cadavers.10e0130201201510.1371/journal.pone.0130201446632026067226Search in Google Scholar
Damann F.E., William D.E., Layton A.C.: Potential use of bacterial community succession in decaying human bone for estimating postmortem interval. J. Forensic Sci. 60, 844–850 (2015)DamannF.E.WilliamD.E.LaytonA.C.Potential use of bacterial community succession in decaying human bone for estimating postmortem interval.60844850201510.1111/1556-4029.1274425808627Search in Google Scholar
Dash H.R., Das S.: Thanatomicrobiome and epinecrotic community signatures for estimation of post-mortem time inter val in human cadaver. Appl. Microbiol. Biot. 104, 9497–9512 (2020)DashH.R.DasS.Thanatomicrobiome and epinecrotic community signatures for estimation of post-mortem time inter val in human cadaver.10494979512202010.1007/s00253-020-10922-333001249Search in Google Scholar
Dautartas A., Kenyhercz M.W., Vidoli G.M., Jantz L.M., Mundorff A., Steadman D.W., Differential decomposition among pig, rabbit and human remains. J. Forensic Sci. 63, 1673–1683 (2018)DautartasA.KenyherczM.W.VidoliG.M.JantzL.M.MundorffA.SteadmanD.W.Differential decomposition among pig, rabbit and human remains.6316731683201810.1111/1556-4029.1378429603225Search in Google Scholar
Dawson B.M., Barton P.S., Wallman J.F.: Contrasting insect activity and decomposition of pigs and humans in an Australian environment: a preliminary study. Forensic Sci. Int. 316, 110515 (2020)DawsonB.M.BartonP.S.WallmanJ.F.Contrasting insect activity and decomposition of pigs and humans in an Australian environment: a preliminary study.316110515202010.1016/j.forsciint.2020.11051533035794Search in Google Scholar
Dibner H., Valdez C., Carter D.O.: An experiment to characterize the decomposer community associated with carcasses (Sus scrofa domesticus) on Oahu, Hawaii. J. Forensic Sci. 64, 1412–1420 (2019)DibnerH.ValdezC.CarterD.O.An experiment to characterize the decomposer community associated with carcasses (Sus scrofa domesticus) on Oahu, Hawaii.6414121420201910.1111/1556-4029.1400930664801Search in Google Scholar
Dickson G.C., Vass A.A.: Death is in the air: confirmation of decomposition without a corpse. Forensic Sci. Int. 301, 149–159 (2019)DicksonG.C.VassA.A.Death is in the air: confirmation of decomposition without a corpse.301149159201910.1016/j.forsciint.2019.05.00531153992Search in Google Scholar
Duerkop B.A., Hooper L.V.: Resident viruses and their interactions with the immune system. Nat. Immunol. 14, 654–659 (2013)DuerkopB.A.HooperL.V.Resident viruses and their interactions with the immune system.14654659201310.1038/ni.2614376023623778792Search in Google Scholar
Dupuy A.K., David M.S., Li L., Heider T.N., Peterson J.D., Montano E.A., Dongari-Bagtzoglou A., Diaz P.I., Strausbaugh L.D.: Redefining of the human oral mycobiome with improved practices in amplicon-based taxonomy: discovery of Malassezia as a prominent commensal. Plos One, 9, e90899 (2014)DupuyA.K.DavidM.S.LiL.HeiderT.N.PetersonJ.D.MontanoE.A.Dongari-BagtzoglouA.DiazP.I.StrausbaughL.D.Redefining of the human oral mycobiome with improved practices in amplicon-based taxonomy: discovery of Malassezia as a prominent commensal.9e90899201410.1371/journal.pone.0090899394869724614173Search in Google Scholar
Dworecka-Kaszak B.: Mycobiome – a cross – talk between fungi and their host. XVI Conference DIGMOL 2015, Molecular biology in diagnostics if infectious disease and biotechnology, Warszawa, 2015, s. 67–71Dworecka-KaszakB.XVI Conference DIGMOL 2015, Molecular biology in diagnostics if infectious disease and biotechnologyWarszawa2015s.6771Search in Google Scholar
Efenberger M., Wódz K., Brzezińska-Błaszczyk E.: Archeony – istotny składnik mikrobiomu człowieka. Przegl. Lek. 71, 346–351 (2014)EfenbergerM.WódzK.Brzezińska-BłaszczykE.Archeony – istotny składnik mikrobiomu człowieka.713463512014Search in Google Scholar
Fancher J.P., Aitkenhead-Peterson J.A., Farris T., Mix K., Schwab A.P., Wescott D.J., Hamilton M.D.: An evaluation of soil chemistryinhumancadaverdecompositionisland:potentialfor estimating postmortem interval. Forensic Sci. Int. 279, 130–139 (2017)FancherJ.P.Aitkenhead-PetersonJ.A.FarrisT.MixK.SchwabA.P.WescottD.J.HamiltonM.D.An evaluation of soil chemistryinhumancadaverdecompositionisland:potentialfor estimating postmortem interval.279130139201710.1016/j.forsciint.2017.08.00228866239Search in Google Scholar
Fernández-Rodríguez A., Cohen M.C. et al.: Post-mortem microbiology in sudden death: sampling protocols proposed in different clinical settings. Clin. Microbiol. Infect. 25, 570–579 (2019)Fernández-RodríguezA.CohenM.C.et alPost-mortem microbiology in sudden death: sampling protocols proposed in different clinical settings.25570579201910.1016/j.cmi.2018.08.00930145399Search in Google Scholar
Finley S.J., Benbow M.E., Javan G.T.: Microbial communities associated with human decomposition and their potential use as postmortem clocks. Int. J. Legal Med. 129, 623–632 (2015)FinleyS.J.BenbowM.E.JavanG.T.Microbial communities associated with human decomposition and their potential use as postmortem clocks.129623632201510.1007/s00414-014-1059-025129823Search in Google Scholar
Finley S.J., Pechal J.L., Benbow M.E., Robertson B.K., Javan G.T.: Microbial signatures of cadaver gravesoil during decomposition. Microb. Ecol. 71, 524–529 (2016)FinleyS.J.PechalJ.L.BenbowM.E.RobertsonB.K.JavanG.T.Microbial signatures of cadaver gravesoil during decomposition.71524529201610.1007/s00248-015-0725-126748499Search in Google Scholar
Forger L.V., Woolf M.S., Simmons T.L., Swall J.L., Singh B.: A eukaryotic community succession based method for postmortem interval (PMI) estimation of decomposing porcine remains. Forensic Sci. Int. 302, 109838 (2019)ForgerL.V.WoolfM.S.SimmonsT.L.SwallJ.L.SinghB.A eukaryotic community succession based method for postmortem interval (PMI) estimation of decomposing porcine remains.302109838201910.1016/j.forsciint.2019.05.05431233889Search in Google Scholar
Frank D.N., Feazel L.M., Bessesen M.T., Price C.S., Janoff E.N., Pace N.R.: The human nasal microbiota and Staphylococcus aureus carriage. Plos One, 5, e10598 (2010)FrankD.N.FeazelL.M.BessesenM.T.PriceC.S.JanoffE.N.PaceN.R.The human nasal microbiota and Staphylococcus aureus carriage.5e10598201010.1371/journal.pone.0010598287179420498722Search in Google Scholar
Frederickx C., Dekeirsschieter J., Verheggen F.J., Haubruge E.: Responses of Lucilia sericata Meigen (diptera: Calliphoridae) to cadaveric volatile organic compounds. J. Forensic Sci. 57, 386–390 (2012)FrederickxC.DekeirsschieterJ.VerheggenF.J.HaubrugeE.Responses of Lucilia sericata Meigen (diptera: Calliphoridae) to cadaveric volatile organic compounds.57386390201210.1111/j.1556-4029.2011.02010.x22150206Search in Google Scholar
Fu X., Guo J., Finkelbergs D., He J., Zha L., Guo Y., Cai J.: Fungal succession during mammalian cadaver decomposition and potential forensic implications. Sci. Rep. 9, 12907 (2019)FuX.GuoJ.FinkelbergsD.HeJ.ZhaL.GuoY.CaiJ.Fungal succession during mammalian cadaver decomposition and potential forensic implications.912907201910.1038/s41598-019-49361-0673390031501472Search in Google Scholar
Grice E.A., Serge J.A.: The skin microbiome. Nat. Rev. Microbiol. 9, 244–253 (2011)GriceE.A.SergeJ.A.The skin microbiome.9244253201110.1038/nrmicro2537353507321407241Search in Google Scholar
Handke J., Procopio N., Buckley M., Van Der Meer D., Williams G., Caar M., Williams A.: Successive bacterial colonisation of pork and its implications for forensic investigations. Forensic Sci. Int. 281, 1–8 (2017)HandkeJ.ProcopioN.BuckleyM.Van Der MeerD.WilliamsG.CaarM.WilliamsA.Successive bacterial colonisation of pork and its implications for forensic investigations.28118201710.1016/j.forsciint.2017.10.02529080415Search in Google Scholar
Harrison L., Kooienga E., Speights C., Tomberlin J., Lashley M., Barton B., Jordan H.: Microbial succession from a subsequent secondary death event following mass mortality. BMC Microbiol. 20, 309 (2020)HarrisonL.KooiengaE.SpeightsC.TomberlinJ.LashleyM.BartonB.JordanH.Microbial succession from a subsequent secondary death event following mass mortality.20309202010.1186/s12866-020-01969-3755703733050884Search in Google Scholar
Hauther K.A., Cobaugh K.L., Jantz L.M., Sparer T.E., DeBruyn J.M.: Estimating time since death from postmortem human gut microbial communities. J. Forensic Sci. 60, 1234–1240 (2015)HautherK.A.CobaughK.L.JantzL.M.SparerT.E.DeBruynJ.M.Estimating time since death from postmortem human gut microbial communities.6012341240201510.1111/1556-4029.1282826096156Search in Google Scholar
Hitosugi M. et al.: Fungican beausefulforensictool. Legal Med. 8, 240–242 (2006)HitosugiM.et alFungican beausefulforensictool.8240242200610.1016/j.legalmed.2006.04.00516798051Search in Google Scholar
Hoffmann C., Dollive S., Grunberg S., Chen J., Li H., Wu G.D., Lewis J.D., Bushman F.D.: Archaea and fungi of the human gut microbiome: correlations with diet and bacterial residents. Plos One, 8, e66019 (2013)HoffmannC.DolliveS.GrunbergS.ChenJ.LiH.WuG.D.LewisJ.D.BushmanF.D.Archaea and fungi of the human gut microbiome: correlations with diet and bacterial residents.8e66019201310.1371/journal.pone.0066019368460423799070Search in Google Scholar
Hoffmann A.R., Proctor L.M., Surette M.G., Suchodolski J.S.: The microbiome: the trillions of microorganisms that maintain health and cause disease in humans and companion animals. Vet. Pathol. 53, 10–21 (2016)HoffmannA.R.ProctorL.M.SuretteM.G.SuchodolskiJ.S.The microbiome: the trillions of microorganisms that maintain health and cause disease in humans and companion animals.531021201610.1177/030098581559551726220947Search in Google Scholar
Holland K.T., Bojar R.A.: Cosmetics: what is their influence on the skin microflora? Am. J. Clin. Dermatol. 3, 445–449 (2002)HollandK.T.BojarR.A.Cosmetics: what is their influence on the skin microflora?3445449200210.2165/00128071-200203070-00001Search in Google Scholar
Hooper L.V., Gordon J.I.: Commensal host – bacterial relationships in the gut. Science, 292, 1115–1118 (2001)HooperL.V.GordonJ.I.Commensal host – bacterial relationships in the gut.29211151118200110.1126/science.1058709Search in Google Scholar
Hopkins D.W., Wiltshire P.E.J., Turner B.D.: Microbial characteristics of soils from graves: an investigation at the interface of soil microbiology and forensic science. Appl. Soil Ecol. 14, 283–288 (2000)HopkinsD.W.WiltshireP.E.J.TurnerB.D.Microbial characteristics of soils from graves: an investigation at the interface of soil microbiology and forensic science.14283288200010.1016/S0929-1393(00)00063-9Search in Google Scholar
Hyde E.R., Haarmann D.P., Lynne A.M., Bucheli S.R., Petrosino J.F.: The living dead: bacterial community structure of a cadaver at the onset and end of the bloat stage of decomposition. Plos One, e77733 (2013)HydeE.R.HaarmannD.P.LynneA.M.BucheliS.R.PetrosinoJ.F.The living dead: bacterial community structure of a cadaver at the onset and end of the bloat stage of decomposition.e77733201310.1371/journal.pone.0077733381376024204941Search in Google Scholar
Hyde E.R., Haarmann D.P., Petrosino J.F., Lynne A.M., Bucheli S.R.: Initial insights into bacterial succession during human decomposition. Int. J. Legal Med. 129, 661–671 (2015)HydeE.R.HaarmannD.P.PetrosinoJ.F.LynneA.M.BucheliS.R.Initial insights into bacterial succession during human decomposition.129661671201510.1007/s00414-014-1128-425431049Search in Google Scholar
Iancu L., Junkins E.N., Necula-Petrareanu G., Purcarea C.: Characterizing forensically important insect and microbial community colonization patterns in buried remains. Sci. Rep. 8, 15513 (2018)IancuL.JunkinsE.N.Necula-PetrareanuG.PurcareaC.Characterizing forensically important insect and microbial community colonization patterns in buried remains.815513201810.1038/s41598-018-33794-0619561530341329Search in Google Scholar
Ishii K., Hitosugi M., Kido M., Yaguchi T., Nishimura K., Hosoya T., Tokudome S.: Analysis of fungi detected in human cadavers. Legal Med. 8, 188–190 (2006)IshiiK.HitosugiM.KidoM.YaguchiT.NishimuraK.HosoyaT.TokudomeS.Analysis of fungi detected in human cadavers.8188190200610.1016/j.legalmed.2005.12.00616516528Search in Google Scholar
Javan G.T., Can I., Finley S.J., Soni S.: The apoptotic thanatotranscriptome associated with the liver of cadavers. Forensic Sci. Med. Phatol. 11, 509–516 (2015)JavanG.T.CanI.FinleyS.J.SoniS.The apoptotic thanatotranscriptome associated with the liver of cadavers.11509516201510.1007/s12024-015-9704-626318598Search in Google Scholar
Javan G.T., Finley S.J., Abidin Z., Mulle J.G.: The thanatomicrobiome: a missing piece of the microbial puzzle of death. Front. Microbiol. 7, 225 (2016)JavanG.T.FinleyS.J.AbidinZ.MulleJ.G.The thanatomicrobiome: a missing piece of the microbial puzzle of death.7225201610.3389/fmicb.2016.00225476470626941736Search in Google Scholar
Javan G.T., Finley S.J., Can I., Wilkinson J.E., Hanson J.D., Tarone A.M.: Human thanatomicrobiome succession and time since death. Sci. Rep. 6, 29598 (2016)JavanG.T.FinleyS.J.CanI.WilkinsonJ.E.HansonJ.D.TaroneA.M.Human thanatomicrobiome succession and time since death.629598201610.1038/srep29598494413227412051Search in Google Scholar
Javan G.T., Finley S.J., Smith T., Miller J., Wilkinson J.E.: Cadaver thanatomicrobiome signatures: the ubiquitous nature of clostridium species in human decomposition. Front. Microbiol. 8, 2096 (2017)JavanG.T.FinleyS.J.SmithT.MillerJ.WilkinsonJ.E.Cadaver thanatomicrobiome signatures: the ubiquitous nature of clostridium species in human decomposition.82096201710.3389/fmicb.2017.02096567011329163394Search in Google Scholar
Javan G.T., Finley S.J., Tuomisto S., Hall A., Benbow M.E., Mills D.E.: An interdisciplinary review of thanatomicrobiome in human decomposition. Forensic Sci. Med. Pat. 15, 75–83 (2019)JavanG.T.FinleyS.J.TuomistoS.HallA.BenbowM.E.MillsD.E.An interdisciplinary review of thanatomicrobiome in human decomposition.157583201910.1007/s12024-018-0061-030519986Search in Google Scholar
Javan G.T., Kwon I., Finley S.J., Lee Y.: Progression of thanatophagyincadaver brainandhearttissues. Biochem. Biophys. Rep. 5, 152–159 (2016)JavanG.T.KwonI.FinleyS.J.LeeY.Progression of thanatophagyincadaver brainandhearttissues.51521592016Search in Google Scholar
Jennifer M., DeBruyn J.M., Hauther K.A.: Postmortem succession of gut microbial communities in deceased human subjects. PeerJ, 5, 3437 (2017)JenniferM.DeBruynJ.M.HautherK.A.Postmortem succession of gut microbial communities in deceased human subjects.53437201710.7717/peerj.3437547057928626612Search in Google Scholar
Johnson H.R., Trinidad D.D., Guzman S., Khan Z., Parziale J.V., DeBruyn J.M., Lents N.H.: Machine learning approach for using the postmortem skin microbiome to estimate the postmortem interval. Plos One, 11, e0167370 (2016)JohnsonH.R.TrinidadD.D.GuzmanS.KhanZ.ParzialeJ.V.DeBruynJ.M.LentsN.H.Machine learning approach for using the postmortem skin microbiome to estimate the postmortem interval.11e0167370201610.1371/journal.pone.0167370517913028005908Search in Google Scholar
Junkins E.N., Speck M., Cartera D.O.: The microbiology, pH, and oxidation reduction potential of larval masses in decomposing carcasses on Oahu, Hawaii. J. Forensic Leg. Med. 67, 37–48 (2019)JunkinsE.N.SpeckM.CarteraD.O.The microbiology, pH, and oxidation reduction potential of larval masses in decomposing carcasses on Oahu, Hawaii.673748201910.1016/j.jflm.2019.08.00131419763Search in Google Scholar
Kaszubinski S.F., Receveur J.P., Wydra B., Smiles K., Wallace J.R., Babcock N.J., Weatherbee C.R., Benbow M.E.: Cold case experiment demonstrates the potential utility of aquatic microbial community assembly in estimating a postmortem submersion interval. J. Forensic Sci. 65, 1210–1220 (2020)KaszubinskiS.F.ReceveurJ.P.WydraB.SmilesK.WallaceJ.R.BabcockN.J.WeatherbeeC.R.BenbowM.E.Cold case experiment demonstrates the potential utility of aquatic microbial community assembly in estimating a postmortem submersion interval.6512101220202010.1111/1556-4029.1430332073664Search in Google Scholar
Krakowiak O., Nowak R.: Mikroflora przewodu pokarmowego człowieka – znaczenie, rozwój, modyfikacje. Postępy Fitoterapii, 3, 193–200 (2015)KrakowiakO.NowakR.Mikroflora przewodu pokarmowego człowieka – znaczenie, rozwój, modyfikacje.31932002015Search in Google Scholar
Lang J.M., Erb R., Pechal J.L., Wallace J.R., McEwan R.W., Benbow M.E.: Microbial biofilm community variation in flowing habitats: potential utility as bioindicators of postmortem submersion intervals. Microorganisms, 4, 1 (2016)LangJ.M.ErbR.PechalJ.L.WallaceJ.R.McEwanR.W.BenbowM.E.Microbial biofilm community variation in flowing habitats: potential utility as bioindicators of postmortem submersion intervals.41201610.3390/microorganisms4010001502950627681897Search in Google Scholar
Lawrence K.E., Lam K.C., Morgun A., Shulzhenko N., Löhr C.V.: Effect of temperature and time on the thanatomicrobiome of the cecum, ileum, kidney, and lung of domestic rabbits. J. Vet. Diagn. Invest. 31, 155–163 (2019)LawrenceK.E.LamK.C.MorgunA.ShulzhenkoN.LöhrC.V.Effect of temperature and time on the thanatomicrobiome of the cecum, ileum, kidney, and lung of domestic rabbits.31155163201910.1177/1040638719828412683882330741115Search in Google Scholar
Lecuit M., Eloit M.: The human virome: new tools and concept. Trends Microbiol. 21, 510–515 (2013)LecuitM.EloitM.The human virome: new tools and concept.21510515201310.1016/j.tim.2013.07.001717252723906500Search in Google Scholar
Li H., Xu J. et al.: Molecular characterization of gut microbial shift in SD rats after death for 30 days. Arch. Microbiol. 202, 1763–1773 (2020)LiH.XuJ.et alMolecular characterization of gut microbial shift in SD rats after death for 30 days.20217631773202010.1007/s00203-020-01889-w32350549Search in Google Scholar
Liu Q., Sun Q., Liu Y., Zhou L., Zheng N., Liu L.: Bioluminescent assay of microbial ATP in postmortem tissues for the estimation of postmortem interval. J. Huazhong Univ. Sci. 29, 679–683 (2009)LiuQ.SunQ.LiuY.ZhouL.ZhengN.LiuL.Bioluminescent assay of microbial ATP in postmortem tissues for the estimation of postmortem interval.29679683200910.1007/s11596-009-0601-720037806Search in Google Scholar
Ma Q., Fonseca A., Liu W., Fields A.T., Pimsler M.L., Spindola A.F., Tarone A.M., Crippen T.L., Tomberlin J.K., Wood T.K.: Proteus mirabilis interkingdom swarming signals attract blow flies. ISME J. 6, 1356–1366 (2012)MaQ.FonsecaA.LiuW.FieldsA.T.PimslerM.L.SpindolaA.F.TaroneA.M.CrippenT.L.TomberlinJ.K.WoodT.K.Proteus mirabilis interkingdom swarming signals attract blow flies.613561366201210.1038/ismej.2011.210337964322237540Search in Google Scholar
Malinowska M., Tokarz-Deptuła B., Deptuła W.: Mikrobiom człowieka. Post. Mikrobiol. 56, 33–42 (2017)MalinowskaM.Tokarz-DeptułaB.DeptułaW.Mikrobiom człowieka.5633422017Search in Google Scholar
Malinowska M., Tokarz-Deptuła B., Deptuła W.: Mikrobiom układu oddechowego w warunkach fizjologicznych i patologicznych. Post. Mikrobiol. 55, 279–283 (2016)MalinowskaM.Tokarz-DeptułaB.DeptułaW.Mikrobiom układu oddechowego w warunkach fizjologicznych i patologicznych.552792832016Search in Google Scholar
Mann R.W., Bass W.M., Meadows L.: Time since death and decomposition of the human body: variables and observations in case and experimental field studies. J. Forensic Sci. 35, 103–111 (1990)MannR.W.BassW.M.MeadowsL.Time since death and decomposition of the human body: variables and observations in case and experimental field studies.35103111199010.1520/JFS12806JSearch in Google Scholar
Maujean G., Guinet T., Fanton L., Malicier D.: The interest of postmortem bacteriology in putrefied bodies. J. Forensic Sci. 58, 1069–1070 (2013)MaujeanG.GuinetT.FantonL.MalicierD.The interest of postmortem bacteriology in putrefied bodies.5810691070201310.1111/1556-4029.1215523551205Search in Google Scholar
Metcalf J.L., Xu Z.Z., Weiss S., Lax S., Treuren W.V.: Microbial community assembly and metabolic function during mammalian corpse decomposition. Science, 351, 6269 (2016)MetcalfJ.L.XuZ.Z.WeissS.LaxS.TreurenW.V.Microbial community assembly and metabolic function during mammalian corpse decomposition.3516269201610.1126/science.aad264626657285Search in Google Scholar
Metcalf J.L.: Estimating the postmortem interval using microbes: knowledge gaps and a path to technology adoption. Forensic Sci. Int. Gen. 38, 211–218 (2019)MetcalfJ.L.Estimating the postmortem interval using microbes: knowledge gaps and a path to technology adoption.38211218201910.1016/j.fsigen.2018.11.00430448529Search in Google Scholar
Micozzi M.S.: Experimental study of postmortem change under field conditions: effects of freezing, thawing and mechanical injury. J. Forensic Sci. 31, 953–961 (1986)MicozziM.S.Experimental study of postmortem change under field conditions: effects of freezing, thawing and mechanical injury.31953961198610.1520/JFS11103JSearch in Google Scholar
Nash A.K., Petrosino J.F. et al.: The gut mycobiome of the human microbiome project healthy kohort. Microbiome, 5, 153 (2017)NashA.K.PetrosinoJ.F.et alThe gut mycobiome of the human microbiome project healthy kohort.5153201710.1186/s40168-017-0373-4570218629178920Search in Google Scholar
Park C.H., Lee S.K.: Exploring esophageal microbiomes in esophageal diseases: a systematic review. J. Neurogastroenterol. Motil. 26, 171–179 (2020)ParkC.H.LeeS.K.Exploring esophageal microbiomes in esophageal diseases: a systematic review.26171179202010.5056/jnm19240717650732235026Search in Google Scholar
Paulino L.C., Tseng C.T., Strober B.E., Blaser M.J.: Molecular analysis of fungal microbiota in samples from healthy human skin and psoriatic lesion. J. Clin. Microbiol. 44, 2933–2941 (2006)PaulinoL.C.TsengC.T.StroberB.E.BlaserM.J.Molecular analysis of fungal microbiota in samples from healthy human skin and psoriatic lesion.4429332941200610.1128/JCM.00785-06159463416891514Search in Google Scholar
Pechal J.L., Schmidt C.J., Jordan H.R., Benbow M.E.: A large-scale survey of the postmortem human microbiome, and its potential to provide insight into the living health condition. Sci. Rep. 8, 5724 (2018)PechalJ.L.SchmidtC.J.JordanH.R.BenbowM.E.A large-scale survey of the postmortem human microbiome, and its potential to provide insight into the living health condition.85724201810.1038/s41598-018-23989-w589354829636512Search in Google Scholar
Pechal J.L., Schmidt C.J., Jordan H.R., Benbow M.E.: Frozen: thawing and its effect on the postmortem microbiome in two pediatric cases. J. Forensic Sci. 62, 1399–1405 (2017)PechalJ.L.SchmidtC.J.JordanH.R.BenbowM.E.Frozen: thawing and its effect on the postmortem microbiome in two pediatric cases.6213991405201710.1111/1556-4029.1341928120409Search in Google Scholar
Pedersen H.K., Gudmundsdottir V., Nielsen H.B., Hyotylainen T., Nielsen T., Jensen B.A., et al.: Human gut microbes impact host serum metabolome and insulin sensitivity. Nature, 535, 376–381 (2016)PedersenH.K.GudmundsdottirV.NielsenH.B.HyotylainenT.NielsenT.JensenB.A.Human gut microbes impact host serum metabolome and insulin sensitivity.535376381201610.1038/nature1864627409811Search in Google Scholar
Procopio N., Ghignone S., Williams A., Chamberlain A., Mello A., Buckley M.: Metabarcoding to investigate changes in soil microbial communities within forensic burial contexts. Forensic Sci. Int. Gen. 39, 73–85 (2019)ProcopioN.GhignoneS.WilliamsA.ChamberlainA.MelloA.BuckleyM.Metabarcoding to investigate changes in soil microbial communities within forensic burial contexts.397385201910.1016/j.fsigen.2018.12.00230594064Search in Google Scholar
Procopio N., Ghignone S., Voyron S., Chiapello M., Williams A., Chamberlain A., Mello A., Buckley M.: Soil fungal communities investigated by metabarcoding within simulated forensic burial contexts. Front. Microbiol. 11, 1686 (2020)ProcopioN.GhignoneS.VoyronS.ChiapelloM.WilliamsA.ChamberlainA.MelloA.BuckleyM.Soil fungal communities investigated by metabarcoding within simulated forensic burial contexts.111686202010.3389/fmicb.2020.01686739327232793158Search in Google Scholar
Santiago-Rodriguez T.M., Fornaciari G., Luciani S., Toranzos G.A., Marota I., Giuffra V., Cano R.J.: Gut microbiome and putative resistome of Inca and Italian nobility mummies. Genes, 8, 310 (2017)Santiago-RodriguezT.M.FornaciariG.LucianiS.ToranzosG.A.MarotaI.GiuffraV.CanoR.J.Gut microbiome and putative resistome of Inca and Italian nobility mummies.8310201710.3390/genes8110310570422329112136Search in Google Scholar
Sidrim J.C., Moreira Filho R.E., Cordeiro R.A., Rocha M.F.G., Caetano E.P., Monteiro A.J., Brilhante R.S.N.: Fungal microbiota dynamics as a postmortem investigation tool: focus on Aspergillus, Penicillium and Candida species. J. Appl. Microbiol. 108, 1751–1756 (2010)SidrimJ.C.Moreira FilhoR.E.CordeiroR.A.RochaM.F.G.CaetanoE.P.MonteiroA.J.BrilhanteR.S.N.Fungal microbiota dynamics as a postmortem investigation tool: focus on AspergillusPenicillium and Candida species.10817511756201010.1111/j.1365-2672.2009.04573.x19863685Search in Google Scholar
Singh B., Minick K.J., Strickland M.S., Wickings K.G., Crippen T.L., Tarone A.M., Benbow M.E., Sufrin N., Tomberlin J.K., Pechal J.L.: Temporal and spatial impact of human cadaver decomposition on soil bacterial and arthropod community structure and function. Front. Microbiol. 8, 2616 (2017)SinghB.MinickK.J.StricklandM.S.WickingsK.G.CrippenT.L.TaroneA.M.BenbowM.E.SufrinN.TomberlinJ.K.PechalJ.L.Temporal and spatial impact of human cadaver decomposition on soil bacterial and arthropod community structure and function.82616201710.3389/fmicb.2017.02616575850129354106Search in Google Scholar
Spagnolo E.V., Stassi C., Mondello C., Zerbo S., Milone L., Argo A.: Forensic microbiology applications: a systematic review. Leg. Med. 36, 73–80 (2019)SpagnoloE.V.StassiC.MondelloC.ZerboS.MiloneL.ArgoA.Forensic microbiology applications: a systematic review.367380201910.1016/j.legalmed.2018.11.00230419494Search in Google Scholar
Stokes K.L., Forbes S.L., Tibbett M.: Human versus animal: contrasting decomposition dynamics of mammalian analogues in experimental taphonomy. J. Forensic Sci. 58, 583–591 (2013)StokesK.L.ForbesS.L.TibbettM.Human versus animal: contrasting decomposition dynamics of mammalian analogues in experimental taphonomy.58583591201310.1111/1556-4029.1211523550805Search in Google Scholar
Strużycka I.: The oral microbiome in dental caries. Pol. J. Microbiol. 63, 127–135 (2014)StrużyckaI.The oral microbiome in dental caries.63127135201410.33073/pjm-2014-018Search in Google Scholar
Thomas T.B., Finley S.J., Wilkinson J.E., Wescott D.J., Gorski A., Javan G.T.: Postmortem microbial communities in burial soil layers of skeletonized humans. Leg. Med. 49, 43–49 (2017)ThomasT.B.FinleyS.J.WilkinsonJ.E.WescottD.J.GorskiA.JavanG.T.Postmortem microbial communities in burial soil layers of skeletonized humans.494349201710.1016/j.jflm.2017.05.00928527363Search in Google Scholar
Thompson C.R., Brogan R.S., Scheifele L.Z., Rivers D.B.: Bacterial interactions with necrophagous flies. Ann. Entomol. Soc. Am. 106, 799–809 (2013)ThompsonC.R.BroganR.S.ScheifeleL.Z.RiversD.B.Bacterial interactions with necrophagous flies.106799809201310.1603/AN12057Search in Google Scholar
Tranchida M.C., Centeno N.D., Cabello M.N.: Soil fungi: their potential use as a forensic tool. J. Forensic Sci. 59, 785–789 (2014)TranchidaM.C.CentenoN.D.CabelloM.N.Soil fungi: their potential use as a forensic tool.59785789201410.1111/1556-4029.1239124502190Search in Google Scholar
Tranchida M.C., Centeno N.D., Stenglein S.A., Cabello M.N.: First record of Talaromyces udagawae in soil related to decomposing human remains in Argentina. Rev. Argent. Microbiol. 48, 86–90 (2016)TranchidaM.C.CentenoN.D.StengleinS.A.CabelloM.N.First record of Talaromyces udagawae in soil related to decomposing human remains in Argentina.488690201610.1016/j.ram.2015.10.00226766627Search in Google Scholar
Tuccia F., Zurgani E., Bortolini S., Vanin S.: Experimental evaluation on the applicability of necrobiome analysis in forensic veterinary science. MicrobiologyOpen, 8, e00828 (2019)TucciaF.ZurganiE.BortoliniS.VaninS.Experimental evaluation on the applicability of necrobiome analysis in forensic veterinary science.8e00828201910.1002/mbo3.828674112330861327Search in Google Scholar
Tuomisto S., Pessi T., Collin P., Vuento R., Aittoniemi J., Karhunen P.J.: Changes in gut bacterial populations and their translocation into liver and ascites in alcoholic liver cirrhotics. BMC gastroenterol. 14, 40 (2014)TuomistoS.PessiT.CollinP.VuentoR.AittoniemiJ.KarhunenP.J.Changes in gut bacterial populations and their translocation into liver and ascites in alcoholic liver cirrhotics.1440201410.1186/1471-230X-14-40399605824564202Search in Google Scholar
Turnbaugh P.J., Ley R.E., Hamady M., Fraser-Liggett C.M., Knight R., Gordon J.I.: The human microbiome project. Nature, 449, 804–810 (2007)TurnbaughP.J.LeyR.E.HamadyM.Fraser-LiggettC.M.KnightR.GordonJ.I.The human microbiome project.449804810200710.1038/nature06244370943917943116Search in Google Scholar
Vogel H., Shukla S.P., Engl T., Weiss B., Fischer R., Steiger S., Heckel D.G., Kaltenpoth M., Vilcinskas A.: The digestive and defensive basis of carcass utilization by the burying beetle and its microbiota. Nat. Commun. 9, 15186 (2017)VogelH.ShuklaS.P.EnglT.WeissB.FischerR.SteigerS.HeckelD.G.KaltenpothM.VilcinskasA.The digestive and defensive basis of carcass utilization by the burying beetle and its microbiota.915186201710.1038/ncomms15186543610628485370Search in Google Scholar
Wilson A.S., O’Keefe S.J.D. et al.: Diet and the human gut microbiome: an international review. Dig. Dis. Sci. 65, 723–740 (2020)WilsonA.S.O’KeefeS.J.D.et alDiet and the human gut microbiome: an international review.65723740202010.1007/s10620-020-06112-w711780032060812Search in Google Scholar
Zhao Y., Jaber V., Lukiw W.J.: Secretory products of the human gl tract microbiome and their potential impact on Alzheimer’s disease (AD): detection of lipopolysaccharide (LPS) in AD hippocampus. Front. Cell. Infect. Microbiol. 7, 318 (2017)ZhaoY.JaberV.LukiwW.J.Secretory products of the human gl tract microbiome and their potential impact on Alzheimer’s disease (AD): detection of lipopolysaccharide (LPS) in AD hippocampus.7318201710.3389/fcimb.2017.00318550472428744452Search in Google Scholar
Zhou W., Bian Y.: Thanatomicrobiome composition profiling as a tool for forensic investigation. Forensic Sci. Res. 3, 105–110 (2018)ZhouW.BianY.Thanatomicrobiome composition profiling as a tool for forensic investigation.3105110201810.1080/20961790.2018.1466430619710030483658Search in Google Scholar
Zhou X., Brown C., Abdo Z., Davis C.C., Hansmann M.A., Joyce P., Foster J.A., Forney L.J.: Differences in the decomposition of vaginal microbial communities found in healthy Caucasian and Black women. ISME J. 1, 121–133 (2007)ZhouX.BrownC.AbdoZ.DavisC.C.HansmannM.A.JoyceP.FosterJ.A.ForneyL.J.Differences in the decomposition of vaginal microbial communities found in healthy Caucasian and Black women.1121133200710.1038/ismej.2007.1218043622Search in Google Scholar