Non-coding RNA Generated following Lariat Debranching Mediates Targeting of AID to DNA.

Transcription through immunoglobulin switch (S) regions is essential for class switch recombination (CSR), but no molecular function of the transcripts has been described. Likewise, recruitment of activation-induced cytidine deaminase (AID) to S regions is critical for CSR; however, the underlying mechanism has not been fully elucidated. Here, we demonstrate that intronic switch RNA acts in trans to target AID to S region DNA. AID binds directly to switch RNA through G-quadruplexes formed by the RNA molecules. Disruption of this interaction by mutation of a key residue in the putative RNA-binding domain of AID impairs recruitment of AID to S region DNA, thereby abolishing CSR. Additionally, inhibition of RNA lariat processing leads to loss of AID localization to S regions and compromises CSR; both defects can be rescued by exogenous expression of switch transcripts in a sequence-specific manner. These studies uncover an RNA-mediated mechanism of targeting AID to DNA.

An interbacterial NAD(P)(+) glycohydrolase toxin requires elongation factor Tu for delivery to target cells.

Type VI secretion (T6S) influences the composition of microbial communities by catalyzing the delivery of toxins between adjacent bacterial cells. Here, we demonstrate that a T6S integral membrane toxin from Pseudomonas aeruginosa, Tse6, acts on target cells by degrading the universally essential dinucleotides NAD(+) and NADP(+). Structural analyses of Tse6 show that it resembles mono-ADP-ribosyltransferase proteins, such as diphtheria toxin, with the exception of a unique loop that both excludes proteinaceous ADP-ribose acceptors and contributes to hydrolysis. We find that entry of Tse6 into target cells requires its binding to an essential housekeeping protein, translation elongation factor Tu (EF-Tu). These proteins participate in a larger assembly that additionally directs toxin export and provides chaperone activity. Visualization of this complex by electron microscopy defines the architecture of a toxin-loaded T6S apparatus and provides mechanistic insight into intercellular membrane protein delivery between bacteria.

A DNA break- and phosphorylation-dependent positive feedback loop promotes immunoglobulin class-switch recombination.

The ability of activation-induced cytidine deaminase (AID) to efficiently mediate class-switch recombination (CSR) is dependent on its phosphorylation at Ser38; however, the trigger that induces AID phosphorylation and the mechanism by which phosphorylated AID drives CSR have not been elucidated. Here we found that phosphorylation of AID at Ser38 was induced by DNA breaks. Conversely, in the absence of AID phosphorylation, DNA breaks were not efficiently generated at switch (S) regions in the immunoglobulin heavy-chain locus (Igh), consistent with a failure of AID to interact with the endonuclease APE1. Additionally, deficiency in the DNA-damage sensor ATM impaired the phosphorylation of AID at Ser38 and the interaction of AID with APE1. Our results identify a positive feedback loop for the amplification of DNA breaks at S regions through the phosphorylation- and ATM-dependent interaction of AID with APE1.

Ataxia Telangiectasia Mutated and MSH2 Control Blunt DNA End Joining in Ig Class Switch Recombination.

Class-switch recombination (CSR) produces secondary Ig isotypes and requires activation-induced cytidine deaminase (AID)-dependent DNA deamination of intronic switch regions within the IgH (Igh) gene locus. Noncanonical repair of deaminated DNA by mismatch repair (MMR) or base excision repair (BER) creates DNA breaks that permit recombination between distal switch regions. Ataxia telangiectasia mutated (ATM)-dependent phosphorylation of AID at serine 38 (pS38-AID) promotes its interaction with apurinic/apyrimidinic endonuclease 1 (APE1), a BER protein, suggesting that ATM regulates CSR through BER. However, pS38-AID may also function in MMR during CSR, although the mechanism remains unknown. To examine whether ATM modulates BER- and/or MMR-dependent CSR, Atm-/- mice were bred to mice deficient for the MMR gene mutS homolog 2 (Msh2). Surprisingly, the predicted Mendelian frequencies of Atm-/-Msh2-/- adult mice were not obtained. To generate ATM and MSH2-deficient B cells, Atm was conditionally deleted on an Msh2-/- background using a floxed ATM allele (Atmf) and B cell-specific Cre recombinase expression (CD23-cre) to produce a deleted ATM allele (AtmD). As compared with AtmD/D and Msh2-/- mice and B cells, AtmD/DMsh2-/- mice and B cells display a reduced CSR phenotype. Interestingly, Sµ-Sγ1 junctions from AtmD/DMsh2-/- B cells that were induced to switch to IgG1 in vitro showed a significant loss of blunt end joins and an increase in insertions as compared with wild-type, AtmD/D, or Msh2-/- B cells. These data indicate that the absence of both ATM and MSH2 blocks nonhomologous end joining, leading to inefficient CSR. We propose a model whereby ATM and MSH2 function cooperatively to regulate end joining during CSR through pS38-AID.

Unveiling Intrinsic Bulk Photovoltaic Effect in Atomically Thin ReS2.

The bulk photovoltaic effect (BPVE) offers a promising avenue to surpass the efficiency limitations of current solar cell technology. However, disentangling intrinsic and extrinsic contributions to photocurrent remains a significant challenge. Here, we fabricate high-quality, lateral devices based on atomically thin ReS2 with minimal contact resistance, providing an optimal platform for distinguishing intrinsic bulk photovoltaic signals from other extrinsic photocurrent contributions originating from interfacial effects. Our devices exhibit large bulk photovoltaic performance with intrinsic responsivities of ∼1 mA/W in the visible range, without the need for external tuning knobs such as strain engineering. Our experimental findings are supported by theoretical calculations. Furthermore, our approach can be extrapolated to investigate the intrinsic BPVE in other noncentrosymmetric van der Waals materials, paving the way for a new generation of efficient light-harvesting devices.

Comparative study of 3D-T2WI vs. 3D-T2-FLAIR MRI in displaying human meningeal lymphatics vessels.

AIM: Various magnetic resonance imaging (MRI) sequences can be utilized to visualize human meningeal lymphatic vessels (MLVs) for investigating the associations between MLVs and central nervous system (CNS) disorders. This study aimed to compare the quality of contrast-enhanced 3D-T2WI and 3D-T2-fluid-attenuated inversion recovery (FLAIR) MRI sequences to display human MLVs. MATERIALS AND METHODS: Sixty-two patients (27 males, 35 females; mean age 55.8 ± 14.9 years) underwent 3D-T2WI and 3D-T2-FLAIR scan in combination with Gd-DTPA injection to show MLVs. RESULTS: (1) The positivity rates of the 3D-T2WI sequence were 98.4%, 29.0%, and 46.8%, around the dural sinus, middle meningeal artery, and ethmoid sinus, respectively. The positivity rates of the 3D-T2-FLAIR sequence were 100%, 48.4%, and 66.1%, respectively. The positivity rate was significantly higher with the 3D-T2-FLAIR sequence compared with the 3D-T2WI sequence for the middle meningeal artery and ethmoid sinus regions (p < 0.05). (2) In patients with brain lesions and intracranial space-occupying lesions, the positivity rate was significantly higher with the 3D-T2-FLAIR sequence compared with the 3D-T2WI sequence for the middle meningeal artery and ethmoid sinus regions (p < 0.05). (3) The mean cross-sectional areas of MLVs around the dural sinus, middle meningeal artery, and ethmoid sinus were all higher using the 3D-T2-FLAIR sequence compared with the 3D-T2WI sequence at all three sites (p < 0.01). (4) The signal intensity was significantly higher using the 3D-T2-FLAIR sequence compared with the 3D-T2WI sequence around the dural sinus and ethmoid sinus (p < 0.001). CONCLUSION: The 3D-T2-FLAIR sequence contrast-enhanced scan showed superior visualization of MLVs compared with the 3D-T2WI sequence.

Analysis of growth performance and carcass and meat quality of different crossbreeds of Cherry Valley duck.

1. Duck breeding and production are facing great opportunities in China, as the market for small-sized high-quality duck is rapidly expanding. Therefore, breeding the most suitable genetic stock has become an important goal.2. This study assessed body and carcass weight, slaughter rate and meat quality of offspring of three cross combinations; Cherry Valley duck (CV♂) × Small-sized Pekin duck (PK♀), CV♂×Taiwan white duck (TW♀), CV♂×Putian white duck (PT♀) and the corresponding pure lines at 56 d of age. These 420 ducks were raised in seven separate groups (10 pens/group, 3♂+3♀/pen).3. Body and carcass weights were significantly lower in the three cross combinations than CV ducks (P = 0.042 and P = 0.012). Abdominal fat was lowest in CV♂×PK♀, whereas the breast and the leg muscle weights were significantly higher in CV♂×PK♀ compared to CV♂×TW♀ and CV♂×PT♀ (P = 0.018 and P = 0.023). No difference was observed in the visceral tissues among the three cross combinations or compared to CV ducks.4. The performance indicators suggested that CV♂×PK♀, CV♂×TW♀ and CV♂×PT♀ cross combinations are best suited for segmented duck meat, featured duck meat and whole-duck processing, respectively.

The uncharacterized SANT and BTB domain-containing protein SANBR inhibits class switch recombination.

Class switch recombination (CSR) is the process by which B cells switch production from IgM/IgD to other immunoglobulin isotypes, enabling them to mount an effective immune response against pathogens. Timely resolution of CSR prevents damage due to an uncontrolled and prolonged immune response. While many positive regulators of CSR have been described, negative regulators of CSR are relatively unknown. Using an shRNA library screen targeting more than 28,000 genes in a mouse B cell line, we have identified a novel, uncharacterized protein of 82kD (KIAA1841, NM_027860), which we have named SANBR (SANT and BTB domain regulator of CSR), as a negative regulator of CSR. The purified, recombinant BTB domain of SANBR exhibited characteristic properties such as homodimerization and interaction with corepressor proteins, including HDAC and SMRT. Overexpression of SANBR inhibited CSR in primary mouse splenic B cells, and inhibition of CSR is dependent on the BTB domain while the SANT domain is largely dispensable. Thus, we have identified a new member of the BTB family that serves as a negative regulator of CSR. Future investigations to identify transcriptional targets of SANBR in B cells will reveal further insights into the specific mechanisms by which SANBR regulates CSR as well as fundamental gene regulatory activities of this protein.

AID Phosphorylation Regulates Mismatch Repair-Dependent Class Switch Recombination and Affinity Maturation.

Activation-induced cytidine deaminase (AID) generates U:G mismatches in Ig genes that can be converted into untemplated mutations during somatic hypermutation or DNA double-strand breaks during class switch recombination (CSR). Null mutations in UNG and MSH2 demonstrate the complementary roles of the base excision repair (BER) and mismatch repair pathways, respectively, in CSR. Phosphorylation of AID at serine 38 was previously hypothesized to regulate BER during CSR, as the AID phosphorylation mutant, AID(S38A), cannot interact with APE1, a BER protein. Consistent with these findings, we observe a complete block in CSR in AIDS38A/S38AMSH2-/- mouse B cells that correlates with an impaired mutation frequency at 5'Sµ. Similarly, somatic hypermutation is almost negligible at the JH4 intron in AIDS38A/S38AMSH2-/- mouse B cells, and, consistent with this, NP-specific affinity maturation in AIDS38A/S38AMSH2-/- mice is not significantly elevated in response to NP-CGG immunization. Surprisingly, AIDS38A/S38AUNG-/- mouse B cells also cannot complete CSR or affinity maturation despite accumulating significant mutations in 5'Sµ as well as the JH4 intron. These data identify a novel role for phosphorylation of AID at serine 38 in mismatch repair-dependent CSR and affinity maturation.

An aggregation model of cockroaches with fast-or-slow motion dichotomy.

We propose a mathematical model, namely a reaction-diffusion system, to describe social behaviour of cockroaches. An essential new aspect in our model is that the dispersion behaviour due to overcrowding effect is taken into account as a counterpart to commonly studied aggregation. This consideration leads to an intriguing new phenomenon which has not been observed in the literature. Namely, due to the competition between aggregation towards areas of higher concentration of pheromone and dispersion avoiding overcrowded areas, the cockroaches aggregate more at the transition area of pheromone. Moreover, we also consider the fast reaction limit where the switching rate between active and inactive subpopulations tends to infinity. By utilising improved duality and energy methods, together with the regularisation of heat operator, we prove that the weak solution of the reaction-diffusion system converges to that of a reaction-cross-diffusion system.

Rapid Denaturing Organic Digestion Method for Targeted Protein Identification and Characterization.

Bottom-up mass spectrometry-based protein analysis methods employing protease digestion are routinely used to identify and characterize proteins with high specificity and sensitivity. Method performance is generally measured by sequence coverage capability and the total number of characteristic peptides identified, when compared to predicted databases. Limitations to commonly used solvent-based digestion methods currently employed include long digestion times (18-24 h or more), leading to protease autolysis, which also precludes automation, decreases sensitivity, and increases both intra- and inter-day performance variability. This report describes the development and validation of a simple, 5 min tryptic denaturing organic digestion (DOD) method for use with tandem mass spectrometry in bottom-up protein identification and characterization. It has been evaluated across select protein toxins and diagnostic clinical protein targets, substantially improving digestion performance when compared to other solution-based and enzyme-immobilized methods. The method was compared to two currently used bottom-up methods, the 24 h filter-aided sample prep (FASP) and Flash Digest (1 and 4 h) methods. Single proteins used to compare the methods included the ricin light chain, ricin heavy chain, ricin holotoxin, serotype A Clostridium botulinum toxin, Staphylococcus enterotoxin B, ribonuclease A, and thyroglobulin. In tests, across the proteins investigated, the 5 min DOD digestion method resulted in sequence coverages ranging from 55 to 100%, with relatively high reproducibility and precision; results were better than or equal to FASP method results and were greatly enhanced when compared to Flash method results. Importantly, DOD method intra- and inter-day precision was much improved as compared to results for both FASP and Flash digestions. These data indicated that the DOD method, when compared to the FASP and Flash Digest methods, dramatically reduced digestion time, while maintaining or improving the ability to detect and characterize targeted proteins, and reduced analytical variability for tryptic digestion, resulting in markedly faster and more precise analyses.

Specific recruitment of protein kinase A to the immunoglobulin locus regulates class-switch recombination.

Immunoglobulin class-switch recombination (CSR) requires activation-induced cytidine deaminase (AID). Deamination of DNA by AID in transcribed switch (S) regions leads to double-stranded breaks in DNA that serve as obligatory CSR intermediates. Here we demonstrate that the catalytic and regulatory subunits of protein kinase A (PKA) were specifically recruited to S regions to promote the localized phosphorylation of AID, which led to binding of replication protein A and subsequent propagation of the CSR cascade. Accordingly, inactivation of PKA resulted in considerable disruption of CSR because of decreased AID phosphorylation and recruitment of replication protein A to S regions. We propose that PKA nucleates the formation of active AID complexes specifically on S regions to generate the high density of DNA lesions required for CSR.

Cutting Edge: ATM Influences Germinal Center Integrity.

The DNA damage response protein ATM has long been known to influence class switch recombination in ex vivo-cultured B cells. However, an assessment of B cell-intrinsic requirement of ATM in humoral responses in vivo was confounded by the fact that its germline deletion affects T cell function, and B:T cell interactions are critical for in vivo immune responses. In this study, we demonstrate that B cell-specific deletion of ATM in mice leads to reduction in germinal center (GC) frequency and size in response to immunization. We find that loss of ATM induces apoptosis of GC B cells, likely due to unresolved DNA lesions in cells attempting to undergo class-switch recombination. Accordingly, suboptimal GC responses in ATM-deficient animals are characterized by decreased titers of class-switched Abs and decreased rates of somatic hypermutation. These results unmask the critical B cell-intrinsic role of ATM in maintaining an optimal GC response following immunization.

T2-weighted, apparent diffusion coefficient and 18F-FDG PET histogram analysis of rectal cancer after preoperative chemoradiotherapy.

BACKGROUND: The aim of our study was to investigate the correlation among T2-weighted (T2w) images, apparent diffusion coefficient (ADC) maps, 18F-fluorodeoxyglucose (18F-FDG) positron emission tomography (PET) images, histogram analysis and the pathological response in locally advanced rectal cancer (LARC) after preoperative chemoradiotherapy (pCRT). METHODS: Patients with LARC were prospectively enrolled between February 2015 and August 2018 and underwent PET/magnetic resonance imaging (MRI). MRI included T2w and diffusion-weighted imaging (DWI)-sequences. ADC maps and PET images were matched to the T2w images. Voxel-based standardized uptake values (SUVs,) ADC and T2w-signal-intensity values were collected from the volumes of interest (VOIs) and mean, skewness and kurtosis were calculated. Spearman's correlation coefficient was applied to evaluate the correlation among the variables and tumor regression grade (TRG), T stage, N stage and fibrosis. RESULTS: Twenty-two patients with biopsy-proven LARC in the low or mid rectum were enrolled [17 males, mean age was 69 years (range 49-85 years)]. Seven patients experienced complete regression (TRG1). A significant positive correlation was found between SUV mean values (ρ = 0.480; p = 0.037) and TRG. No other significant correlations were found. CONCLUSIONS: Histogram analysis of SUV values is a predictor of TRG in LARC.

Development and optimization of orthotopic liver metastasis xenograft mouse models in uveal melanoma.

BACKGROUND: Patients with metastatic uveal melanoma (MUM) in the liver usually die within 1 year. The development of new treatments for MUM has been limited by the lack of diverse MUM cell lines and appropriate animal models. We previously reported that orthotopic xenograft mouse models established by direct injection of MUM cells into the liver were useful for the analysis associated with tumor microenvironment in the liver. However, considering that patients with UM metastasize to the liver hematogenously, direct liver injection model might not be suitable for investigation on various mechanisms of liver metastasis. Here, we aim to establish new orthotopic xenograft models via hematogenous dissemination of tumor cells to the liver, and to compare their characteristics with the hepatic injection model. We also determine if hepatic tumors could be effectively monitored with non-invasive live imaging. METHODS: tdtTomate-labeled, patient-derived MUM cells were injected into the liver, spleen or tail vein of immunodeficient NSG mice. Tumor growth was serially assessed with In Vivo Imaging System (IVIS) images once every week. Established hepatic tumors were evaluated with CT scan and then analyzed histologically. RESULTS: We found that splenic injection could consistently establish hepatic tumors. Non-invasive imaging showed that the splenic injection model had more consistent and stronger fluorescent intensity compared to the hepatic injection model. There were no significant differences in tumor growth between splenic injection with splenectomy and without splenectomy. The splenic injection established hepatic tumors diffusely throughout the liver, while the hepatic injection of tumor cells established a single localized tumor. Long-term monitoring of tumor development showed that tumor growth, tumor distribution in the liver, and overall survival depended on the number of tumor cells injected to the spleen. CONCLUSION: We established a new orthotopic hepatic metastatic xenograft mouse model by splenic injection of MUM cells. The growth of orthotopic hepatic tumors could be monitored with non-invasive IVIS imaging. Moreover, we evaluated the therapeutic effect of a MEK inhibitor by using this model. Our findings suggest that our new orthotopic liver metastatic mouse model may be useful for preclinical drug screening experiments and for the analysis of liver metastasis mechanisms.

Systematic analysis of copy-number variations associated with early pregnancy loss.

OBJECTIVES: Embryonic numerical and structural chromosomal abnormalities are the most common cause of early pregnancy loss. However, the role of submicroscopic copy-number variations (CNVs) in early pregnancy loss is unclear, and little is known about the critical regions and candidate genes for miscarriage, because of the large size of structural chromosomal abnormalities. The aim of this study was to identify potential miscarriage-associated submicroscopic CNVs and critical regions of large CNVs as well as candidate genes for miscarriage. METHODS: Over a 5-year period, 5180 fresh miscarriage specimens were investigated using quantitative fluorescent polymerase chain reaction/CNV sequencing or chromosomal microarray analysis. Statistically significant submicroscopic CNVs were identified by comparing the frequency of recurrent submicroscopic CNVs between cases and a published control cohort. Furthermore, genes within critical regions of miscarriage-associated CNVs were prioritized by integrating the Residual Variation Intolerance Score and the human gene expression dataset for identification of potential miscarriage candidate genes. RESULTS: Results without significant maternal-cell contamination were obtained in 5003 of the 5180 (96.6%) cases. Clinically significant chromosomal abnormalities were identified in 59.1% (2955/5003) of these cases. Three recurrent submicroscopic CNVs (microdeletions in 22q11.21, 2q37.3 and 9p24.3p24.2) were significantly more frequent in miscarriage cases, and were considered to be associated with miscarriage. Moreover, 44 critical regions of large CNVs were observed, including 14 deletions and 30 duplications. There were 309 genes identified as potential miscarriage candidate genes through gene-prioritization analysis. CONCLUSIONS: We identified potential miscarriage candidate CNVs and genes. These data demonstrate the importance of CNVs in the etiology of miscarriage and highlight the importance of ongoing analysis of CNVs in the study of miscarriage. Copyright © 2019 ISUOG. Published by John Wiley & Sons Ltd.

Serum Procalcitonin, White Blood Cell and Hypersensitive C-reactive Protein Combined with Age Established a New Prediction Model in Predicting ICU Admission in Adult Community-Acquired Pneumonia (CAP) Patients.

BACKGROUND: CAP is the most common cause of death in infectious diseases in developing countries, while also an important cause of death and morbidity in developed countries. In recent years, CURB-65 (or CRB-65) and pneumonia severity index (PSI) scoring systems have been widely used in the prognosis scoring system of CAP. However, each of them has some shortcomings in predicting ICU admission in CAP patients. The aim of this study is to analyze serum inflammatory biomarkers combined age to established a new prediction model in predicting ICU admission in CAP patients. METHODS: This is a retrospective study. The enrolled CAP patients received serum inflammatory biomarker tests, including procalcitonin (PCT), white blood cell count (WBC), hypersensitive C-reactive protein (hs-CRP), and erythrocyte sedimentation rate (ESR). Body temperature and age were also recorded. The main outcome measures were ICU admission. Univariate analysis and binary logistic regression analysis were used to explore the in-dependent risk factors which could be components of a new predicting model for ICU admission in CAP patients. Receiver operating characteristic curves (ROC) were used to evaluate the sensitivity and specificity of the new model, which consisted of the combination of all independent risk factors in predicting the main outcomes. RESULTS: Initially, 246 CAP patients were admitted to general wards, 61 of whom were subsequently transferred to ICU (61/246). Age, PCT, WBC, and hs-CRP were independent risk factors for subsequent admission to ICU for CAP patients in general wards. The AUC of the ROC curve of new prediction model (the joint model consists of age, PCT, WBC, and hs-CRP) was 0.93 (95% CI 0.85 - 0.96), the sensitivity and specificity were 85.2% and 88.1%, respectively. CONCLUSIONS: Serum inflammatory biomarkers combined age have high specificity and sensitivity in predicting ICU admission in adult CAP patients.

Neutrophil-to-Lymphocyte Ratio Improves the Accuracy and Sensitivity of Pneumonia Severity Index in Predicting 30-Day Mortality of CAP Patients.

BACKGROUND: The pneumonia severity index (PSI) scoring system is one of the tools used to evaluate and predict the prognosis of patients with community-acquired pneumonia (CAP). Although PSI has been widely used in clinical studies of pneumonia, it is still rare to combine it with blood indexes to predict the prognosis of pneumonia. Neutrophil-to-lymphocyte ratio (NLR) is a promising candidate predictor of mortality in CAP patients. The aim of this study was to investigate the efficacy of pneumonia severity index combined with NLR in predicting 30-day mortality in CAP patients. METHODS: We conducted a retrospective study. We analyzed data on 400 non-immune individuals over the age of 18 in this study. All patients received blood routine measurement and PSI score calculation after admission. The primary outcome measures were mortality and survival in CAP patients. The sensitivity and specificity of PSI score, NLR, and the combination of PSI score and NLR in predicting 30-day mortality were assessed using the subject operating characteristic curve (ROC). RESULTS: Data from 400 patients were analyzed, in which the 30-day mortality was 10.5% (42/400). The AUC of NLR and PSI in predicting 30-day mortality of CAP patients were 0.81 (95% CI 0.73 - 0.89) and 0.94 (95% CI 0.90 - 0.98), respectively, with statistically significant differences (p = 0.00). The sensitivity and specificity of NLR were 0.80 and 0.7, respectively. The sensitivity and specificity of PSI were 0.78 and 0.94, respectively. The combined AUC of the two indicators for predicting death in CAP patients was 0.95 (95% CI 0.92 - 0.99), and the sensitivity and specificity were 0.85 and 0.94, respectively. CONCLUSIONS: Neutrophil-to-lymphocyte ratio improves the accuracy and sensitivity of the pneumonia severity index in predicting 30-day mortality of CAP patients.

Human symbionts inject and neutralize antibacterial toxins to persist in the gut.

The human gut microbiome is a dynamic and densely populated microbial community that can provide important benefits to its host. Cooperation and competition for nutrients among its constituents only partially explain community composition and interpersonal variation. Notably, certain human-associated Bacteroidetes--one of two major phyla in the gut--also encode machinery for contact-dependent interbacterial antagonism, but its impact within gut microbial communities remains unknown. Here we report that prominent human gut symbionts persist in the gut through continuous attack on their immediate neighbors. Our analysis of just one of the hundreds of species in these communities reveals 12 candidate antibacterial effector loci that can exist in 32 combinations. Through the use of secretome studies, in vitro bacterial interaction assays and multiple mouse models, we uncover strain-specific effector/immunity repertoires that can predict interbacterial interactions in vitro and in vivo, and find that some of these strains avoid contact-dependent killing by accumulating immunity genes to effectors that they do not encode. Effector transmission rates in live animals can exceed 1 billion events per minute per gram of colonic contents, and multiphylum communities of human gut commensals can partially protect sensitive strains from these attacks. Together, these results suggest that gut microbes can determine their interactions through direct contact. An understanding of the strategies human gut symbionts have evolved to target other members of this community may provide new approaches for microbiome manipulation.