Early Settlement Research Articles

Effect of Probiotic Supplementation on the Gut Microbiota Composition of Infants Delivered by Cesarean Section: An Exploratory, Randomized, Open-label, Parallel-controlled Trial.

Infants born via cesarean section (CS) are at an increased risk of immune-related diseases later in life, potentially due to altered gut microbiota. Recent research has focused on the administration of probiotics in the prevention of gut microbiota dysbiosis in neonates delivered by CS. This study was performed to investigate the effects of probiotic supplementation on the gut microbiota of CS-delivered infants. Thirty full-term neonates delivered by CS were randomized into the intervention (supplemented orally with a probiotic containing Bifidobacterium longum, Lactobacillus acidophilus, and Enterococcus faecalis for 2weeks) and control groups. Stool samples were collected at birth and 2weeks and 42days after birth. The composition of the gut microbiota was analyzed using 16S rRNA sequencing technology. The applied bacterial strains were abundant in the CS-delivered infants supplemented with probiotics. Probiotics increased the abundance of some beneficial bacteria, such as Bacteroides, Acinetobacter, Veillonella, and Faecalibacterium. Low colonization of Klebsiella, a potentially pathogenic bacterium, was observed in the intervention group. Our results showed that probiotics supplemented immediately after CS enriched the gut microbiota composition and altered the pattern of early gut colonization. registration number NCT05086458.

The first arriving virus shapes within-host viral diversity during natural epidemics.

Viral diversity has been discovered across scales from host individuals to populations. However, the drivers of viral community assembly are still largely unknown. Within-host viral communities are formed through co-infections, where the interval between the arrival times of viruses may vary. Priority effects describe the timing and order in which species arrive in an environment, and how early colonizers impact subsequent community assembly. To study the effect of the first-arriving virus on subsequent infection patterns of five focal viruses, we set up a field experiment using naïve Plantago lanceolata plants as sentinels during a seasonal virus epidemic. Using joint species distribution modelling, we find both positive and negative effects of early season viral infection on late season viral colonization patterns. The direction of the effect depends on both the host genotype and which virus colonized the host early in the season. It is well established that co-occurring viruses may change the virulence and transmission of viral infections. However, our results show that priority effects may also play an important, previously unquantified role in viral community assembly. The assessment of these temporal dynamics within a community ecological framework will improve our ability to understand and predict viral diversity in natural systems.

General and specialized metabolites in peanut roots regulate arbuscular mycorrhizal symbiosis

Arbuscular mycorrhizae (AM) fungi form symbiotic associations with plant roots, providing nutritional benefits and promoting plant growth and defenses against various stresses. Metabolic changes in the roots during AM fungal colonization are key to understanding the development and maintenance of these symbioses. Here, we investigated metabolic changes in the roots of peanut (Arachis hypogaea L.) plants during the colonization and development of AM symbiosis, and compared them to uncolonized roots. The primary changes during the initial stage of AM colonization were in the contents and compositions of phenylpropanoid and flavonoid compounds. These compounds function in signaling pathways that regulate recognition, interactions, and pre-colonization between roots and AM fungi. Flavonoid compounds decreased by 25% when the symbiosis was fully established compared to the initial colonization stage. After AM symbiosis was established, general metabolism strongly shifted toward the formation of lipids, amino acids, carboxylic acids, and carbohydrates. Lipid compounds increased by 8.5% from the pre-symbiotic stage to well-established symbiosis. Lyso-phosphatidylcholines, which are signaling compounds, were only present in AM roots, and decreased in content after the symbiosis was established. In the initial stage of AM establishment, the content of salicylic acid increased two-fold, whereas jasmonic acid and abscisic acid decreased compared to uncolonized roots. The jasmonic acid content decreased in roots after the symbiosis was well established. AM symbiosis was associated with high levels of calcium, magnesium, and D-(+)-mannose, which stimulated seedling growth. Overall, specific metabolites that favor the establishment of AM symbiosis were common in the roots, primarily during early colonization, whereas general metabolism was strongly altered when AM symbiosis was well-established. In conclusion, specialized metabolites function as signaling compounds to establish AM symbiosis. These compounds are no longer produced after the symbiosis between the roots and AM becomes fully established.

Indocyanine green guided sentinel lymph node biopsy may have a high sensitivity for early (T1/T2) colon cancer: A prospective study in Indian patients.

Indocyanine green (ICG) dye guided near infrared fluorescence (NIR) imaging is a promising tool for mapping lymphatics. The aim of this study was to evaluate the role of ICG guided SLN biopsy in Indian colon cancer patients. Forty-eight patients of clinically staged T1-T3 node negative colon cancer underwent laparoscopic/open resection. Patients received colonoscopic peritumoral submucosal ICG injections for laparoscopic (n= 32) and subserosal injections for open resections (n= 16) followed by the detection of SLN using NIR camera. SLNs underwent conventional hematoxylin and eosin (H & E) staging with additional serial sectioning and immunohistochemistry for pancytokeratin antibody (ultra-staging). Detection rate and upstaging rate were the primary end points. Forty-eight patients were recruited. An average of 2.08 ± 1.27 SLNs were identified in 45 patients at a mean time of 8.2 ± 3.68 minutes with a detection rate of 93.75%. Mean age and mean BMI were 59.7 ± 12.54 years and 24.8 ± 4.09 kg/m2 , respectively. Eighteen patients had node positive disease, and SLN was false negative in four of these patients resulting in a sensitivity of 77.77% with a trend towards higher sensitivity for T1-T2 tumours (90% vs. 62.5%, p= 0.068). Upstaging rate was 10%. Negative predictive value (NPV) and accuracy of the procedure were 87.09% and 91.11%, respectively. ICG guided SLN biopsy can identify metastatic lymph nodes in colon cancer patients that can be missed on H & E staging with relatively higher sensitivity for early (T1/T2) tumours.

Three cases of colon cancer in four generations of the Saudi family, caused by endogamous germline mutations.

Various research pieces of evidence have been published in recent years, establishing the increasing prevalence of early colon cancer among young people. In this background, the current study aimed to analyze the reasons behind colon cancer recurrence among endogamous consanguineous cases in four generations of a single Saud family. For this study, the authors conducted the whole-exome sequencing analysis to screen for germline mutations in DNA samples from consanguineous cases within the family. After collecting the colon samples, it was analyzed histologically and immunohistochemically with the help of Breast Cancer antibodies (BRCA2 and 1 correspondingly) and H&M staining (hematoxylin and eosin). For this study, 26 at-risk consanguineous cases were considered. Three cases were diagnosed with malignant colon cancer, two with breast cancer, and 17 with germline mutations, yet remain unaffected by cancerous tumors. The rest, four consanguineous cases, are healthy and non-carriers of the mutations. However, as per the exome analysis outcomes, 15 cases inherited germline mutations in nine genes. Nine substitution mutations were present in six of the nine inherited genes in these inherited germline mutations. Furthermore, it also presented six insertion and deletion frameshift mutations in five of nine inherited genes. The immunohistochemical staining process achieved positive staining outcomes for BRCA1 and 2. Therefore, germline mutations inherited from the nine genes of endogamous consanguineous cases of mutation carriers remain the primary reason behind colon cancer recurrence in the same family.

Identification of donor Bacteroides vulgatus genes encoding proteins that correlate with early colonization following fecal transplant of patients with recurrent Clostridium difficile

Due to suppressive antibiotics, patients with recurrent Clostridium difficile have gut microbial communities that are devoid of most commensal microbes. Studies have shown that most of the failures using fecal microbe transplantation (FMT) for recurrent C. difficile occur during the first 4 weeks following transplantation. To identify features of donor Bacteroides vulgatus that lead to early colonization, we used two data sets that collected fecal samples from recipients at early times points post FMT. The first analysis used the shotgun metagenomic DNA sequencing data set from Aggarwala et al. consisting of 7 FMT donors and 13 patients with recurrent C. difficile with fecal samples taken as early as 24 h post FMT. We identified 2 FMT donors in which colonization of recipients by donor B. vulgatus was detected as early as 24 h post FMT. We examined a second data set from Hourigan et al. that collected fecal samples from C. difficile infected children and identified 1 of 3 FMT that also had early colonization of the donor B. vulgatus. We found 19 genes out of 4911 encoding proteins were unique to the 3 donors that had early colonization. A gene encoding a putative chitobiase was identified that was in a gene complex that had been previously identified to enhance colonization in mice. A gene encoding a unique fimbrillin (i.e., pili) family protein and 17 genes encoding hypothetical proteins were also specific for early colonizing donors. Most of the genes encoding hypothetical proteins had neighboring genes that encoded proteins involved in mobilization or transposition. Finally, analysis of 42 paired fecal samples from the human microbiome project (HMP) found no individuals had all 19 genes while 2 individuals had none of the 19 genes. Based on the results from our study, consideration should be given to the screening of FMT donors for these B. vulgatus genes found to enhance early colonization that would be of benefit to promote colonization following FMT.

Racial disparities in survival of early onset colon cancer (Age

BackgroundEarly-onset colon cancer (EOCC) has increasing incidence and disproportionately affects African-Americans. This analysis aims to compare EOCC survival among Black and White patients after matching relevant socio-demographic factors and stage. MethodsThe 2004–2017 NCDB database was queried for Black and White patients, age<50, who underwent colectomy for adenocarcinoma. A one-to-one match on race was performed based on sociodemographic factors and disease stage (I-IV). Five-year survival differences were analyzed with Cox proportional hazards models. Results5322 Black-White matched pairs were analyzed. Compared to White patients, Black patients averaged more days to surgery (19 ​± ​68 vs 16 days ​± ​32, p ​< ​0.001) and to chemotherapy (63 ​± ​8 vs. 57 ​± ​39, p ​< ​0.001). Black stage III patients were 20% less likely to receive chemotherapy (OR 0.8, 95% CI 0.7–0.9, p ​= ​0.0006), and had a 17% increased rate of death (HR 1.17, 95% CI 1.0–1.3, p ​= ​0.01) after adjusting for sex, comorbidity score, tumor location and chemotherapy. ConclusionsBlack patients with stage 3 EOCC are less likely to receive chemotherapy and have worse survival. Further evaluation is warranted to identify potential factors driving these observed.

Infant gut microbiota colonization: influence of prenatal and postnatal factors, focusing on diet.

Maternal microbiota forms the first infant gut microbial inoculum, and perinatal factors (diet and use of antibiotics during pregnancy) and/or neonatal factors, like intra partum antibiotics, gestational age and mode of delivery, may influence microbial colonization. After birth, when the principal colonization occurs, the microbial diversity increases and converges toward a stable adult-like microbiota by the end of the first 3-5 years of life. However, during the early life, gut microbiota can be disrupted by other postnatal factors like mode of infant feeding, antibiotic usage, and various environmental factors generating a state of dysbiosis. Gut dysbiosis have been reported to increase the risk of necrotizing enterocolitis and some chronic diseases later in life, such as obesity, diabetes, cancer, allergies, and asthma. Therefore, understanding the impact of a correct maternal-to-infant microbial transfer and a good infant early colonization and maturation throughout life would reduce the risk of disease in early and late life. This paper reviews the published evidence on early-life gut microbiota development, as well as the different factors influencing its evolution before, at, and after birth, focusing on diet and nutrition during pregnancy and in the first months of life.

A Unique Śaṅkhalipi (Shell-script) Inscription from Si Thep, Thailand

Inscriptions in the highly calligraphic and still undeciphered śaṅkhalipi or ‘shell script’ have been found by the hundreds in most parts of India except the far south, typically in conjunction with sites and monuments dating from around the Gupta period and succeeding centuries. To date, four specimens have also been discovered in the Indonesian archipelago, in West Java and West Kalimantan (Borneo). Another specimen of śaṅkhalipi inscription, engraved on a pillar and exceptionally ornate, was recently discovered in Thailand at the site of Si Thep, a moated early settlement in Phetchabun Province. The article reviews the historical and cultural contexts of shell-script inscriptions in India and discusses the significance of this remarkable first specimen found in mainland Southeast Asia.

Assessing the Bioreceptivity of Biobased Cladding Materials

Materials exposed to the outdoors are prone to various deterioration processes. Architectural coatings are designed to protect surfaces against environmental and biotic degradation and to provide a decorative layer. The objective of this work was to examine the early colonisers on a diverse set of coated and non-coated biobased façade materials. A set of 33 wood-based cladding materials were exposed to four cardinal directions and monitored in outdoor conditions. The surfaces were sampled using a wet swab and plated on DG-18 agar, which prevents the growth of bacteria and limits the growth of fast-growing fungi. Pure cultures were then isolated and identified through PCR amplification and Sanger sequencing of specific DNA regions/genes. The response of cladding materials to weathering and fungal infestation was assessed. The proposed techniques enabled the identification of features that promote/inhibit fungal colonisation and revealed the preference of certain fungi for specific materials. Both the material type and the climate condition at the exposure site influence fungal colonisation. This study is a starting point for more exhaustive assays that aim to develop a novel coating system based on controlled and optimized fungal biofilm formation, and is proposed as a nature-inspired alternative for the protection of architectonic surfaces.

Gathering Souls: Jesuit Missions in the Spanish Empire

Abstract This article examines two different missionary areas where the Society of Jesus was sent to evangelise the native population: the Andean territories previously under Inca domination and the remote Mariana Islands in the Pacific Rim. The gathering of “other barbarians” living outside “civilised” societies was a tool of early modern colonisers within Europe and beyond. The English did so in sixteenth-century Ireland and the Spanish began reducing the so-called American Indians to new settlements in New Spain and Peru. In this paper, I want to compare the methods used to concentrate the natives of the Viceroyalty of Peru, where the Jesuits actively collaborated, with the borderland mission of the Marianas, where the Jesuits worked as parishioners of a much less sophisticated people: the CHamoru.1 As I will demonstrate, this policy of gathering souls was not an isolated one, but part and parcel of a universalistic principle of spreading God's word that was irremediably embedded in colonial structures of coercion and political control in the Americas and Asia-Pacific.

Breast Cancer Cell Type and Biomechanical Properties of Decellularized Mouse Organs Drives Tumor Cell Colonization.

Tissue engineering has emerged as an indispensable tool for the reconstruction of organ-specific environments. Organ-derived extracellular matrices (ECM) and, especially, decellularized tissues (DCL) are recognized as the most successful biomaterials in regenerative medicine, as DCL preserves the most essential organ-specific ECM properties such as composition alongside biomechanics characterized by stiffness and porosity. Expansion of the DCL technology to cancer biology research, drug development, and nanomedicine is pending refinement of the existing DCL protocols whose reproducibility remains sub-optimal varying from organ to organ. We introduce a facile decellularization protocol universally applicable to murine organs, including liver, lungs, spleen, kidneys, and ovaries, with demonstrated robustness, reproducibility, high purification from cell debris, and architecture preservation, as confirmed by the histological and SEM analysis. The biomechanical properties of as-produced DCL organs expressed in terms of the local and total stiffness were measured using our facile methodology and were found well preserved in comparison with the intact organs. To demonstrate the utility of the developed DCL model to cancer research, we engineered three-dimensional tissue constructs by recellularization representative decellularized organs and collagenous hydrogel with human breast cancer cells of pronounced mesenchymal (MDA-MB-231) or epithelial (SKBR-3) phenotypes. The biomechanical properties of the DCL organs were found pivotal to determining the cancer cell fate and progression. Our histological and scanning electron microscopy (SEM) study revealed that the larger the ECM mean pore size and the smaller the total stiffness (as in lung and ovary), the more proliferative and invasive the mesenchymal cells became. At the same time, the low local stiffness ECMs (ranged 2.8-3.6 kPa) did support the epithelial-like SKBR-3 cells' viability (as in lung and spleen), while stiff ECMs did not. The total and local stiffness of the collagenous hydrogel was measured too low to sustain the proliferative potential of both cell lines. The observed cell proliferation patterns were easily interpretable in terms of the ECM biomechanical properties, such as binding sites, embedment facilities, and migration space. As such, our three-dimensional tissue engineering model is scalable and adaptable for pharmacological testing and cancer biology research of metastatic and primary tumors, including early metastatic colonization in native organ-specific ECM.

Starch grains on human teeth as evidence for 4000 BCE potato consumption at the Cruz Verde site, northern coast of Peru

Cruz Verde, located on the north coast of Peru in the Chicama River Basin, is an artificial mound formed by the continuous disposal of food residues between 4200 and 3800 cal. BC. It is a vital archaeological site for understanding the early maritime community that was established in the coastal areas of Peru during the middle Holocene period. Previous studies focusing on animal remains have shown that a wide range of marine resource uses were flexibly maintained in a changing environment. However, the use of plants by coastal fishermen, which has been reported in recent years at other sites in the same region, was not evident at Cruz Verde. This paper reports on an examination of starch grains preserved in the dental calculus of human teeth excavated from the mound at Cruz Verde, which provides direct evidence of the early consumption of cultivated food plants, such as maize (Zea mays), manioc (Manihot esculenta), squash (Cucurbita sp.), and potatoes (Solanum tuberosum). Not only did the results indicate early use of maize indicated in previous studies, but they also confirmed that the use of potatoes at the site dates back to at least 4000 cal. BC—the oldest example from the coastal region of Peru. The micro-botanical data from Cruz Verde suggest that fishing and plant cultivation were combined in the development process of early settlement. Furthermore, the data on this earliest potato use in the coastal area are significant because they contribute to the empirical foundation of understanding the early relationship with maritime and highland communities during this period.

Fire as high-elevation cold adaptation: An evaluation of fuels and Terminal Pleistocene combustion in the Central Andes

The use of fire constitutes an essential cultural adaptation to cold, and archaeological evidence for fire can be expected in high-latitude and high-elevation regions successfully inhabited by modern humans. At Cuncaicha rockshelter (4480 m above sea level, or masl) in the southern Peruvian Andes, evidence for fire is present from the earliest occupation, dating to the Terminal Pleistocene (∼12,500–11,200 cal BP). Yet, the site contains relatively few identifiable carbonized macrobotanical remains useful for identifying plants employed as combustible fuel. Based on a comprehensive review of nearly 40 early Andean archaeological sites above 2500 masl, little is known about fuels used for combustion. To understand fuel selection strategies at Cuncaicha, we conducted a combustion field experiment, evaluating the three highland plant taxa most likely to have been used as combustible fuels: Polylepis rugulosa (queñua) tree branches, Parastrephia spp. (tola) woody shrubs, and Azorella compacta (yareta) cushion plants. Temperature measurements informed on the combustion characteristics and efficiency of each fuel. We then compared the experimentally-produced fire residues to the geoarchaeological evidence from Cuncaicha. The resinous cushion plant yareta, endemic to the high Andes, may have been the primary fuel used at Cuncaicha based on the experiment outcome and the geoarchaeological evidence. Due to its high-temperature and complete combustion, yareta leaves little to no macrobotanical evidence, thus its identification at other Andean sites may require a multi-methodological approach. Because the geographic range of this plant corresponds with most early archaeological sites in the high Andes, yareta may have been a key resource enabling early settlement throughout the region.

Modeling periodontal host-microbe interactions using vascularized gingival connective tissue equivalents

Gingival connective tissue and its vasculature play a crucial role in the host’s immune response against the periodontal microbiome and serve as a bridge between the oral and systemic environments. However, there is a lack of representative models that mimic the complex features of vascularized gingival connective tissue and its interaction with the periodontal microbiome, hindering our understanding of periodontal health and disease. Towards this pursuit, we present the characterization of vascularized gingival connective tissue equivalents (CTEs) as a model to study the interactions between oral biofilm colonizers and gingival tissues in healthy and diseased states. Whole-mount immunolabeling and label-free confocal reflectance microscopy of human fibrin-based matrix embedded with gingival fibroblasts and microvascular endothelial cells demonstrated the generation of bi-cellular vascularized gingival CTEs. Next, we investigated the response of the vascularized gingival CTEs to early, intermediate, and late oral biofilm colonizers. Despite colonization, the early colonizers did not elicit any significant change in the production of the cytokines and chemokines by the CTEs representative of the commensal and homeostatic state. In contrast, intermediate and late colonizers representing a transition to a diseased state exhibited connective tissue and vascular invasion, and elicited a differential immune response accompanied by increased monocyte migration. The culture supernatants produced by the vascularized gingival CTEs in response to early and intermediate colonizers polarized macrophages towards an immunomodulatory M2-like phenotype which activates and protects the host, while the late colonizers polarized towards a pro-inflammatory M1-like phenotype. Lastly, in silico analysis showed a high strength of associations between the proteins and transcripts investigated with periodontitis and vascular diseases. In conclusion, the vascularized gingival CTEs provide a biomimetic in vitro platform to study host-microbiome interactions and innate immune response in periodontal health and diseased states, which potentially paves the way toward the development and assessment of novel periodontal therapeutics.

Chemotherapy-induced neutropenia elicits metastasis formation in mice by promoting proliferation of disseminated tumor cells

ABSTRACT Chemotherapy is the standard of care for most malignancies. Its tumor debulking effect in adjuvant or neoadjuvant settings is unquestionable, although secondary effects have been reported that paradoxically promote metastasis. Chemotherapy affects the hematopoietic precursors leading to myelosuppression, with neutropenia being the main hematological toxicity induced by cytotoxic therapy. We used renal and lung murine tumor models metastatic to the lung to study chemotherapy-induced neutropenia (CIN) in the metastatic process. Cyclophosphamide and doxorubicin, two myelosuppressive drugs, but not cisplatin, increased the burden of artificial metastases to the lung, by reducing neutrophils. This effect was recapitulated by treatment with anti-Ly6G, the selective antibody-mediated neutrophil depletion that unleashed the formation of lung metastases in both artificial and spontaneous metastasis settings. The increased cancer dissemination was reversed by granulocyte-colony stimulating factor-mediated boosting of neutrophils in combination with chemotherapy. CIN affected the early metastatic colonization of the lung, quite likely promoting the proliferation of tumor cells extravasated into the lung at 24–72 hours. CIN did not affect the late events of the metastatic process, with established metastasis to the lung, nor was there any effect on the release of cancer cells from the primary, whose growth was, in fact, somewhat inhibited. This work suggests a role of neutrophils associated to a common cancer treatment side effect and claims a deep dive into the relationship between chemotherapy-induced neutropenia and metastasis.

Segmented filamentous bacteria-based treatment to elicit protection against Enterobacteriaceae in Layer chickens.

Gut microbes like segmented filamentous bacteria (SFB) play a key role in gut maturation during early life, as demonstrated in humans and mice. Our previous study demonstrated oral inoculation of ileum-spores containing SFB to chickens after hatch increases early SFB gut colonization, which increases immune maturation and resistance to bacteria, like Salmonella, as tested in vitro; however, more studies are needed for treatment optimization and in vivo testing. The objectives of this study were to (1) test a treatment that includes both spores and filamentous SFB, (2) validate antimicrobial ability of the treatment in layer hens in vivo, and (3) elucidate its molecular mechanism. One-day-old specific pathogen-free layers (n = 12 per group) were orally treated with either PBS (CON) or SFB-based treatment (SFB). At 4 days post-inoculation (DPI), both CON and SFB groups were orally challenged with Salmonella Typhimurium. Total Enterobacteriaceae and Salmonella were examined by plating and enumeration in feces at 7,10 and 14 dpi; and in the ileum, cecum, and spleen at 16 dpi in euthanized birds. The presence and levels of SFB were determined from ilea scrapings via microscopy and qPCR, respectively. Relative gene expression of host-derived antimicrobial peptides and cytokines in the distal ileum was determined by RT-qPCR. At 10 and 14 dpi, a significant decrease in total Enterobacteriaceae was observed in the feces of the SFB group. At necropsy, the level of SFB was significantly higher in the SFB group than in the CON group, while a significant decrease in total Enterobacteriaceae and Salmonella was observed in the ceca of the SFB group. RT-qPCR revealed increased expression of β-defensin 14, and cytokines IL-10 and IFNγ. The introduction of SFB at hatch as a prophylactic treatment may benefit commercial partners as well as consumers by reducing the incidence of Enterobacteriaceae in food animals. Reduction of these bacteria in animals would, in turn, increase animal health, productivity, and safety for consumers. Studies to optimize the treatment for poultry industry applications are ongoing in our lab.

Early colonization of sessile megabenthos on electrolytic carbonated structures (Alicante's harbor, Western Mediterranean)

Biofouling of different artificial substrates was studied to determine the differences in biofouling assemblages among different substrates. However, studies on biofouling on natural substrates like electrolytic carbonated ones are lacking. These substrates have a great potential for coral reef restoration in tropical areas and for biofilter construction. Thus, this study was developed to examine the colonization of sessile macrofouling in the port of Alicante (SE Spain, Western Mediterranean) on two types of substrates: electrolytic carbonated and bare steel (as control) over three months of immersion (October 2019–January 2020). The community diversity was studied through different biotic parameters and abundance of assemblages, and preference of organisms according to their status and functional group (active filter feeders). Univariate and multivariate analyses (PERMANOVA and SIMPER) were also applied to examine the differences between carbonate and control substrates. The carbonated substrate had a more structured community and higher abundance, recruitment, and diversity indexes than the bare steel. Moreover, filter feeders (Porifera, Bivalvia, and Ascidiacea) were more abundant, and most of them only appeared in the carbonated substrate. These results show the potential of carbonated structures as biofilters.

Microbiome convergence and deterministic community assembly along successional biocrust gradients on potash salt heaps.

Potash mining, typically performed for agricultural fertilizer production, can create piles of residual salt waste that are ecologically detrimental and difficult to revegetate. Biological soil crusts (biocrusts) have been found growing on and around these heaps, suggesting resilience to the hypersaline environment. We set out to understand the community dynamics of biocrust formation by examining two succesionary salinity gradients at historical mining sites using a high throughput amplicon sequencing. Bare heaps were distinct, with little overlap between sites, and were characterized by high salinity, low nutrient availability, and specialized, low diversity microbial communities, dominated by Halobacteria, Chloroflexia, and Deinococci. 'Initial' stages of biocrust development were dominated by site-specific Cyanobacteria, with significant overlap between sites. Established biocrusts were the most diverse, with large proportions of Alphaproteobacteria, Anaerolineae, and Planctomycetacia. Along the salinity gradient at both sites, salinity decreased, pH decreased, and nutrients and Chlorophyll a increased. Microbiomes between sites converged during succession and community assembly process analysis revealed biocrusts at both sites were dominated by deterministic, niche-based processes; indicating a high degree of phylogenetic turnover. We posit early cyanobacterial colonization is essential for biocrust initiation, and facilitates later establishment of plant and other higher-level biota.

Integrated multi-omic analyses provide insight into colon adenoma susceptibility modulation by the gut microbiota.

Colon cancer onset is strongly associated with the differences in microbial taxa in the gastrointestinal tract. Although recent studies highlight the role of individual taxa, the effect of a complex gut microbiome (GM) on the metabolome and host transcriptome is still unknown. We used a multi-omics approach to determine how differences in the GM affect the susceptibility to adenoma development in a rat model of human colon cancer. Ultra-high performance liquid chromatography mass spectrometry of feces collected prior to observable disease onset identified putative metabolite profiles that likely predict future disease severity. Transcriptome analyses performed after disease onset from normal colonic epithelium and tumor tissues show a correlation between GM and host gene expression. Integrated pathway analyses of the metabolome and transcriptome based on putatively identified metabolic features indicate that bile acid biosynthesis is enriched in rats with high tumors along with increased fatty acid metabolism and mucin biosynthesis. Targeted pyrosequencing of the Pirc allele indicates that the GM alters the mechanism of adenoma development and may drive an epigenetic pathway of tumor suppressor silencing. This study reveals how untargeted metabolomics identifies signatures of susceptibility and integrated analyses uncover pathways of differential mechanisms of loss of tumor suppressor gene function and for potential prevention and therapeutic intervention. IMPORTANCE The association between the gut microbiome and colon cancer is significant but difficult to test in model systems. This study highlights the association of differences in the pathogen-free gut microbiome to changes in the host transcriptome and metabolome that correlate with colon adenoma initiation and development in a rat genetic model of early colon cancer. The utilization of a multi-omics approach integrating metabolomics and transcriptomics reveals differences in pathways including bile acid biosynthesis and fatty acid metabolism. The study also shows that differences in gut microbiomes significantly alter the mechanism of adenoma formation, shifting from genetic changes to epigenetic changes that initiate the early loss of tumor suppressor function. These findings enhance our understanding of the gut microbiome's role in colon cancer susceptibility, offer insights into potential biomarkers and therapeutic targets, and may pave the way for future prevention and intervention strategies.